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E46 M3 (2001-2006) Engine: S54 - Max Hp: 333 hp at 7,900 rpm / 262 lb/ft at 4,900 rpm
Total Produced: 45,000+ - Years Produced: 2001 to 2006.


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Old Sun, Aug-20-2017, 07:31:50 PM   #1
mrgizmo04
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Default E46 M3 misfires and stumbles at low rpm, no codes

Hey fellow enthusiasts. My car (2005 M3, 90K miles) developed some misfire/knock and lack of power at low RPM (idle – 1700RPM), but only after it properly warms up (oil temp getting closer to 200). Idling cold is fine, even idling after warming up is fine, it doesn't try to shut down and the idle does not bounce around and is not too rough. This seemed to develop after a big maintenance kick and changing coils / plugs / injectors / O2 sensors / catback exhaust. At higher RPMs (>1700) the car seems to run fine and feels like it gets the power back and that initial stumble from idle - 1700RPM. Car does not smoke, oil consumption seems minimal, fuel consumption seems down (averaging around 15-16mpg city/highway).

Car throws no fault codes except for "TCU: GPS antenna, open circuit". A long time ago it used to show code "CF DME: Misfiring cyl 3 without cylinder cutout", but has not shown up since I cleared it 4 months ago. Also since I cleared it, I got new coils/spark plugs/injectors/O2 sensors/catback system.

Compression test is fine. Got a Foxwell 510 code scanner, no codes. I am not sure what all the other numbers and abbreviations from the DME scanner mean (too many of them) to come up with a single conclusion.

After much guessing about noise from the clutch, loose exhaust flanges or broken exhaust welds, I started looking at some data on Foxwell 510. The misfire count on the cylinders looks interesting: 8, 3, 30, 3, 3, 4. This is a count for “current drive” which means I was driving the car for ~20 mins (not too hard) to get it warmed up and then idling afterwards to get and record the readout. Most of the misfires happened while idling.

Disconnecting the MAF, it barely stumbles/changes in idle. Should that have idled a lot rougher when disconnected or even shut down? Reconnecting and disconnecting again right afterwards, nothing seems to happen, but not sure how long DME takes to adjust.

Ran a dry compression test after idling the car for a few minutes to warm up: 165, 165, 171, 167, 165, 165, so these seem fine and above the minimum recommended and tight together. One interesting thing here, although not sure it’s that significant is that cyl 3, which has the most misfires has the highest compression (possibly due to carbon build-up)?

Disconnecting each coil one-by-one, the car stumbles and idles rough, so coils/plugs/injectors(?) all good. All 4 O2 sensors new, but not sure if I connected them in the right order (pre vs post-cat) when I was doing maintenance. ICV was cleaned, so was MAF.

Some readouts from the scanner follow here with numbers I think could be suspect in red.

EDK adaptation menu
rise, potentiometer at throttle: 28.3%/V
rise, potentiometer at servomotor: 27.9%/V
throttle air leak: 2kg/h normal? too high?
potentiometer at throttle, zero stop: 0.38V
potentiometer at servomotor, zero stop: 4.17V
max deviation between specified and actual values of throttle position: 3%
Counter, increased EDK duty factor: 1
Counter, controller activation: 36
Counter, controller deactivation: 0
OBDII complete list @idle (unless otherwise noted)
DTC_CNT: 0
FUELSYS1: CL
FUELSYS2: CL
LOAD_PCT: 18.4%
ECT: 151DEG F
SHRTFT1: -6.3->3.1% ok to fluctuate this much?
LONGFT1: 6.3% a bit too high? >5%
SHRTFT2: -0.8%->7% ok to fluctuate this much?
LONGFT1: 6.3% a bit too high? >5%

RPM: 889rpm
VSS: 0mph
SPARKADV: 21.5DEG (increases to 26DEG when rpm increased to 1600)
IAT: 88DEG F
MAF: 0.01LB/S (increases to 0.02LB/S when rpm increased to 1600, and increases to 0.03LB/S when blip the throttle to 2500RPM) should this sense more lb/s?
TP: 0% doesn't seem to change when RPM increased to 1600,
increases to 0.8% when blip the throttle to 2500RPM) is this faulty?

AIR_STAT: OFF
O2 SLOC: B1 S1 2-- AND B2 S1 2--
O2B1 S1: 0.1->0.82V small fluctuation normal?
SHRTFTB1 S1: -3.1%->3.9% is this normal to fluctuate this much?
O2B1 S2: 0.785->0.84V small fluctuation normal?
SHRTFTB1 S2: 99.2% is this normal to be at 99.2%, what should this be?
O2B2 S1: 0.06V->0.755v is this normal to fluctuate this much?
SHRTFTB2 S1: -3.9%->3.9% is this normal to fluctuate this much?
O2B2 S2: 0.725->0.795V small fluctuation normal?
SHRTFTB2 S2: 99.2% is this normal to be at 99.2% same as B1, what should this be?

OBDSUP: OBDII
MIL_DIST: 0miles
Throttle position menu
Throttle potentiometer position 0% (even when increase rpm to 1600) is TPS faulty, should this increase?
servomotor potentiometer position: 0% (even when increase rpm to 1600) is TPS faulty, should this increase?
Throttle potentiometer: 0.4V (even when increase rpm to 1600) is TPS faulty, should this increase?

Servomotor 4.29-4.32V (even when increase rpm to 1600)
EDK actuator, duty factor: 8.15%
Control factor, charge controller: 0.97
EDK specification by DME: 0.00%
Knock Adaptation Menu
Cyl 1: -2.8deg CR, sometimes -3.21
Cyl 2: -1.21deg CR sometimes -1.61
Cyl 3: -0.81deg CR
Cyl 4: -0.41deg CR
Cyl 5: -0.81deg CR
Cyl 6: -2.01deg CR
Have not cleared the adaptations, maybe these need to be cleared, they seem all over the place?
Ignition menu
All cylinders @21.5deg CR at idle
Oxygen Sensor menu
Tank ventilation adaptation, bank1: 1.00
Fuel system, cylinder 1 /3: 1.00
Control factor bank2: 1.02 a little over 1 ok?
Oxygen sensor control, bank2: not active
Mixture adaptation, idle speed, additive, bank2: -0.06ms
Mixture adaptation, multiplicative, part load, bank2: 6.31%
Tank ventilation adaptation, bank2: 1.00
Fuel system, cylinder 4 /6: 1.00
Control factor bank1: 0.38 much less than 1.02 on bank 2, should this be this low?
Oxygen sensor control, bank1: not active
Idle speed control menu
Specified idle speed: 870
Idle controller: Active, sometimes not active
Idle speed control valve, Duty factor: 26.03%
Idle controller: varies -420 to -704.10Nm fluctuation normal?
Idle controller adaptation torque: 4.50Nm
Injection menu
Number of deactivated cylinders: 0
Number of deactivated cylinders DME specific: 0
Duration of injection: 1.6-2.06ms at idle varies slightly between cylinders. These times normal to vary?
Temperature sensor menu (numbers at idle after car has been properly warmed up)
Ambient temperature: 75deg F
Exhaust temperature: 550deg F. Is this too low for a car at operating temperature (oil ~200 degreees)?
Intake air temperature: 115deg F
Coolant temperature engine outlet: 176deg F
Engine oil temperature: 199deg F
Engine outlet temperature sensor: 1.11V
Intake air temperature sensor: 2.46mV
Radiator outlet temperature sensor: 1.67V
Minimum DME temperature: 158deg F

Some potential conclusions.
-Can probably rule out head/head gasket issues based on compression test.
-Valve adjustment coming up and some of the grommets are leaking a bit from previous owner's
work, not sure if this is causing any vacuum leaks.
-Not sure if during all the recent maintenance I incorrectly swapped Pre/Post Cat O2 sensors?
-New Magnaflow catback exhaust could need retightening of flanges, maybe a leak?
-Do not remember this behavior (misfire/knock/lack of power at low RPM when car warm) before
I changed coils/plugs/injectors/O2 sensors and with the old catback exhaust (all were changed together). Do I need to clear adaptations and drive around to see if numbers change?
-Combination of low exhaust temperature 550 (I expected it to be 2x or even 3x the value when
the car is at operating temperature) and some of the B1 and B2 fuel trim numbers being whacky,
could mean that it might be the cats?
-Values on MAF and TP are probably suspect, staying around 0? Could be leading to fuel trims
to be + (lean) since there is probably more air getting into the engine than 0?
-Not sure why this misfire/stumbling on power only happens when car reaches operating temp (not coolant getting to ~halfway mark, which happens rather quickly, but oil temp getting closer to 200 which takes some time) and only in limited RPM range.

I have a youtube video with recording of what it sounds like and some of the other numbers:

Appreciate all the help!

Last edited by mrgizmo04; Sun, Aug-20-2017 at 10:54:26 PM.
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Old Sun, Aug-20-2017, 09:54:24 PM   #2
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Default Re: E46 M3 misfires and stumbles at low rpm, no codes

Jesus H Christ. Tldr. Change plugs/coils. Clean or buy new MAF?
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Old Sun, Aug-20-2017, 10:51:22 PM   #3
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Default Re: E46 M3 misfires and stumbles at low rpm, no codes

Thanks Tbone. I know you said Tldr, I agree, it is long and is not for the faint-hearted. I try to provide as much context as possible and try to list things I have tried (that is partially why it is so long), brand new coils/plugs included and disconnecting each coil separately makes the car stumble and idle rough, which confirms those are good. MAF I cleaned, disconnecting it made the car stumble a bit, however readout numbers for how much air it's sensing seem suspect and low, but not sure if those numbers are normal.

I am doing everything DIY, so looking for some help from anyone who has experienced anything like this.

It could be as simple as me needing to clear adaptations and driving it for a while to normalize things.

Appreciate you taking a look.

Last edited by mrgizmo04; Sun, Aug-20-2017 at 10:57:17 PM.
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Old Sun, Aug-20-2017, 11:44:20 PM   #4
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Default Re: E46 M3 misfires and stumbles at low rpm, no codes

I suspect you don't have your O2 sensors connected correctly - go through some of the header DIYs and they explain which sensor goes where


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Old Mon, Aug-21-2017, 01:52:14 AM   #5
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Default Re: E46 M3 misfires and stumbles at low rpm, no codes

EDK adaptation menu
throttle air leak: 2kg/h normal? too high? Should be fine
SHRTFT1: -6.3->3.1% ok to fluctuate this much? Yes
LONGFT1: 6.3% a bit too high? >5%
SHRTFT2: -0.8%->7% ok to fluctuate this much?
LONGFT1: 6.3% a bit too high? >5%


All the fuel trims should be ok if they're +/- 5, heading towards 10 something could be off but still not a cause for alarm
Fuel trims are also a gauge of how far off your tune is for any mods you've done, it's normal for them to fluctuate with different conditions


MAF: 0.01LB/S (increases to 0.02LB/S when rpm increased to 1600, and increases to 0.03LB/S when blip the throttle to 2500RPM) should this sense more lb/s?

My car idles ~24-30kg/hr (which is the standard measurement for most airflow on this engine), lbs/s is a very large unit

TP: 0% doesn't seem to change when RPM increased to 1600,
increases to 0.8% when blip the throttle to 2500RPM) is this faulty?


Sounds normal, the ICV handles most part throttle so I doub't you'd see much plate angle
O2B1 S1: 0.1->0.82V small fluctuation normal?
SHRTFTB1 S1: -3.1%->3.9% is this normal to fluctuate this much? yes
SHRTFTB1 S2: 99.2% is this normal to be at 99.2%, it could be a fluke with how your meter is reading it, or you have your rear O2s swapped
SHRTFTB2 S2: 99.2% is this normal to be at 99.2% same as B1, what should this be?

SHRTFTB2 S1: -3.9%->3.9% is this normal to fluctuate this much? yes
O2B2 S1: 0.06V->0.755v is this normal to fluctuate this much? yes
O2B2 S2: 0.725->0.795V small fluctuation normal? yes

Throttle potentiometer position 0% (even when increase rpm to 1600) If you rev it higher/harder it should. Try doing a full sweep with just the ignition on to satisfy your curiosity

Knock Adaptation Menu
Cyl 1: -2.8deg CR, sometimes -3.21
Cyl 2: -1.21deg CR sometimes -1.61
Cyl 3: -0.81deg CR
Cyl 4: -0.41deg CR
Cyl 5: -0.81deg CR
Cyl 6: -2.01deg CR
Have not cleared the adaptations Seems pretty standard, usually the front and rear cylinders see more knock retard

Oxygen Sensor menu
Control factor bank2: 1.02 a little over 1 ok? Yes
Control factor bank1: 0.38 much less than 1.02 on bank 2, should this be this low? That is odd, I'd expect it to be higher but it could be your meter

Duration of injection: 1.6-2.06ms at idle varies slightly between cylinders. These times normal to vary? Yes
Exhaust temperature: 550deg F. Is this too low for a car at operating temperature (oil ~200 degreees)? No, it's not under load so there isn't much heat in the exhaust

Some potential conclusions.
-Can probably rule out head/head gasket Probably
-Valve adjustment coming up. Your compression test leads me to believe your valves may be out of adjustment - They're within tolerance across the board but still below spec overall. you did the compression test holding the throttle open right?
-Not sure if during all the recent maintenance I incorrectly swapped Pre/Post Cat O2 sensors? I'd absolutely make sure they're all correct
-New Magnaflow catback exhaust could need retightening of flanges, maybe a leak? Never hurts to double check after heat cycling
- Do I need to clear adaptations Not required but doesn't hurt
-Combination of low exhaust temperature 550 My car usually idles around 400-600*F
-Values on MAF and TP are probably suspect, staying around 0? not immediately
-Not sure why this misfire/stumbling on power only happens when car reaches operating temp (not coolant getting to ~halfway mark, which happens rather quickly, but oil temp getting closer to 200 which takes some time) and only in limited RPM range. It's probably your secondary 02.
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Old Mon, Aug-21-2017, 04:26:19 AM   #6
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Default Re: E46 M3 misfires and stumbles at low rpm, no codes

Exodus - awesome feedback, exactly what I was looking for!

Yes, compression test was done at WOT, but the car was "cold"-ish, I only idled it for a few minutes, if that, to get it a bit warmed up (it sat in the garage for a few days before that).

About the MAF, that is actually great to know that you register ~25kg/h@idle, that is around where I am too then in lb/s, 0.01lb/s is ~16kg/h (I can not see more significant digits on mine, but am sure it's rounding down to 0.01, in reality it might be closer to 0.014, which would put it about 24kg/h). So sounds like MAF is ok. I was hesitant on it because I read somewhere that when you disconnect the MAF the car should REALLY run rough or even stall, but if you look on my youtube video around minute 2:19 when I disconnect the MAF there is very slight hesitation and then it fully recovers back to normal before I reconnect it.

I will definitely check all O2 sensors to make sure they are all in the right places and connected properly. I'll trace where they are pre/post cat and just disconnect each wire at a time, the reader should tell me what it is sensing, so I'll be able to isolate that way. Also to note on O2 sensors, I got mine off amazon (same Bosch part numbers but for fraction of the price of BMW's), not sure if there are known issues with those.

Someone else ("Nathan's DIY Garage" on youtube) suggested that my gas or fuel lines might have water in them or gas just is bad (I use Costco gas). This would make the cylinders misfire, especially one with highest compression (which in my case is cyl 3, which misfires an order of magnitude more than others) since by having water in it, it lowers octane. Worth checking out HEET for $2, so I'll try to get that and run through a tank.

I'll also clear the adaptations, which couldn't hurt.

Valve adjustment, yes, it is just overdue. I'll be doing that soon once I get all the parts to do VANOS and cooling system at same time.

Thank you for your detailed feedback!

01M3Fan - will definitely check them out. Thank you for feedback.
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Old Fri, Sep-01-2017, 04:57:08 AM   #7
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Default Re: E46 M3 misfires and stumbles at low rpm, no codes

Quick update here. All O2 sensors seem to be connected properly and in the right places.

I cleared adaptations and noticed that it seems to idle a bit cleaner. Right after clearing adaptations it seemed to hesitate a bit on the initial start but then straightened out within a few seconds.

I'm guessing clearing adaptations is required after either or any combo of these - coils/plugs/O2 sensors/injectors/catback exhaust so the car can re-sense and re-learn.

Drove it for about 20-25 miles, some hard on the highway, car seems lively, computer registered no misfires when I sat in a parking lot idling afterwards, trying to see if it would get any misfires around 1200-1500RPM like before after properly warming up, it did not. This is the good part.

The bad part - after I parked for 20-30 mins to grab dinner, came back to the parking lot and started it, the idle bounced around 900-1100 for about 10-15 seconds and cyl 3 registered 14 misfires. Shut it down/restarted again, no hesitation idle was steady around 900, drove it home, idled at home for a bit to check the codes/reader, no misfires. Hopefully the computer is still relearning.

Will drive it for a few more days see how it behaves. Some folks suggested that it might take a few drives/a few times of resetting adaptations.

Will provide the next update next week after driving it more and observing behavior.

A lot of the readouts that I have in the first post I also recorded but have to transcribe (don't have time tonight). Some numbers changed for the better. Will try to provide those tomorrow.
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Old Wed, Sep-06-2017, 06:02:06 AM   #8
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Default Re: E46 M3 misfires and stumbles at low rpm, no codes

Hey guys,
So the behavior I described in the previous post (NOT the original post) - after driving the car relatively hard to get it properly warmed up and then parking it to observe behavior at idle and 1200-1500rpm (where a lot of the misfires occurred in the original post), I don't get any misfires and the car seems like it has smooth power delivery at low rpm, whereas in the original post it stumbled at low rpm, so that's the good. The bad is that after shutting the car down for 15-20 mins and then starting it back up, the first 10 seconds or so it hunts around for a smooth idle and bounces around 900-1100 and a few (5-10) misfires register on cylinder 3, and one or two other cylinders register a misfire here and there. This behavior of idle bouncing around for the first ~10secs and misfires registering on cylinder 3 doesn't happen every time I restart the car after a bit of a cool-down, I would say this happens about 50% of the time, the other 50% it starts up normally and idles perfectly normally.

The only difference between the original post and this most-recent behavior is I cleared all adaptations, so now have been driving for a few days, maybe 100 miles total since clearing adaptations. Again, no fault codes are thrown.

Please let me know if anything stands out here. Valve adjustment still pending (a bit overdue), valve cover grommets are a bit leaky (from crappy job by PO), VANOS rebuild still pending.

Below are the numbers I noticed changed between original post (pre-clearing adaptations) vs now (driving a few days after clearing adaptations) with some comments:

EDK adaptation menu
throttle air leak: 0.19kg/h (in original post this was ~2kg/h)
max deviation between specified and actual values of throttle position: 1.8% (in original post was ~3%)
Counter, increased EDK duty factor: 0 (in original post was 1)
Counter, controller activation: 1 (in original post was 36)


OBDII list
ECT: 187DEG F (this seems to be a lot higher than in original post, was 151)

SHRTFT1: -3.1->3.1% FLUCTUATES
LONGFT1: 5.5% (was in low-mid 3s after resetting adaptations which was done a few days ago, now jumped up to 5.5 today, still lower than original post of 6.3%)

SHRTFT2: -3.9%->3.1% FLUCTUATES
LONGFT2: 3.9% (in original post was 6.3%)
IAT: 138DEG F (this seems to be a lot higher than in original post before clearing adaptations of 88)


Knock Adaptation Menu

Overall as some of the cylinders have been registering random misfires on re-start after cooldown, these numbers have been becoming less negative and more positive.
Cyl 1: -2.41deg CR

Cyl 2: -0.81deg CR
Cyl 3: 0.79deg CR (was really close to 0 a few days ago when reset adaptations, today jumped up to 0.79, probably due to some misfires registering on this cylinder over past few days?)
Cyl 4: 0.79deg CR
Cyl 5: -0.01deg CR
Cyl 6: -1.21deg CR


Oxygen Sensor menu
Control factor bank2: 1.00-1.05
Oxygen sensor control, bank2: Active (in original post was not active for some reason)
Mixture adaptation, multiplicative, part load, bank2: 2.93% (in original post was 6.31%)
Control factor bank1: 1.63 (in original post was 0.38)
Oxygen sensor control, bank1: Active (in original post was not active)


Idle speed control menu
Idle controller: -525.40Nm

VANOS menu
Inlet vanos, actual value: 58.90deg CR
Inlet vanos, pilot control by DME: 51.2deg CR

Sensor Gear Adaptations menu

Didn’t include this in original post, but had values ready for the original post, included are current numbers and in parenthesis are numbers before clearing adaptations.
Crankshaft1: 0 degrees/00 (also 0 in original)
Crankshaft2: -1.07 (-1.34 originally)
Crankshaft3: -0.45 (-0.64 originally)
Crankshaft4: 0.02 (-0.23 originally)
Crankshaft5:-1.17 (-1.18 originally)
Crankshaft6: -0.20 (-1.41 originally)
Counter, sensor gear/crankshaft adaptation: 662 (before clearing adaptations, this was really high, 65535)

Basic quantities menu (not provided in original post)
engine speed: 897rpm
engine load: 21.5%
power supply: 13.3V
ambient pressure (sensor in cm) 1016.0
air-mass flow: 21kg/h (different menu from the OBD2 one which shows 0.01lb/s equivalent)
air mass flow sensor: 1.14V
relative opening cross section from throttle body and idle opening: 0.15%
Tank ventilating valve, duty factor: 13.55%
Electric fan, duty factor: 62%
Clocking, electric fuel pump: 5.37ms
Oil level: 91mm
tank fill level: 37L

Oxygen sensor (heater) menu (not provided in original post)
Oxygen sensor heater, before catalytic converter short voltage, bank1: 3.69-3.71V
Oxygen sensor heater, after catalytic converter short voltage, bank1: 3.64-3.66V
Oxygen sensor voltage, before catalytic converter, bank1: 0.1-0.83V
Oxygen sensor voltage, after catalytic converter, bank1: 0.73-0.82V
Oxygen sensor heater, before catalytic converter short voltage, bank2: 3.60-3.63V
Oxygen sensor heater, after catalytic converter short voltage, bank2: 3.63-3.65V
Oxygen sensor voltage, before catalytic converter, bank2: 0.07-0.79V
Oxygen sensor voltage, after catalytic converter, bank2: 0.77-0.82V

Pedal Travel Sensor menu (not provided in original post)
pedal travel sensor, potentiometer 1: 0.00%
pedal travel sensor, potentiometer 2: 0.00%
pedal travel sensor 1, adaptation, zero position: 733.13mV
pedal travel sensor 2, adaptation, zero position: 366.56mV
pedal travel sensor 1, voltage: 737.31mV
pedal travel sensor 2, voltage: 371.1mV

Idle Synchronization Adaptation menu (not provided in original post)
Cyl 1: -76 muS
Cyl 2: -22 muS
Cyl 3: 98 muS
Cyl 4: -41 muS
Cyl 5: -56 muS
Cyl 6: 97 muS

Appreciate the help.
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Old Wed, Sep-06-2017, 10:59:57 PM   #9
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Default Re: E46 M3 misfires and stumbles at low rpm, no codes

i've had the same "warm idle hunting" issue for over 5 years (in fact, it seems to be common on these cars), never was able to figure it out and I don't have any other symptoms. It might just be a red herring and unrelated to your previous issue.
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Old Thu, Sep-07-2017, 05:54:21 AM   #10
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Default Re: E46 M3 misfires and stumbles at low rpm, no codes

Quote:
Originally Posted by Toxic0n View Post
i've had the same "warm idle hunting" issue for over 5 years (in fact, it seems to be common on these cars), never was able to figure it out and I don't have any other symptoms. It might just be a red herring and unrelated to your previous issue.
Mine is not that bad, it doesn't try to surge more than maybe 200rpm. Doesn't try to shut down or anything.

You can see starting @ second 15 in below video is when it starts surging a bit, but then it settles down. Problem is that it doesn't happen with every warm start/restart and it doesn't really last for that long, so hard to figure out what it could be.

https://drive.google.com/file/d/0B6y...ew?usp=sharing

My long term trims just shot up from ~4% to ~8%. I could maybe try to clear adaptations because weather has been erratic here. Normally around 70s/80s, weekend was well into 100s.

Another thing I did/tried - I got a new tank from Shell (normally go with Costco gas), and added HEET to see if it could take out any moisture buildup in the fuel lines. Can't say I noticed anything being better after that.

The only thing I can say with 99% confidence is that clearing adaptations has helped, there are fewer misfires registering than in the past. I try to force the idle via throttle (like in the past) to 1200-1500 and don't get much, maybe 1-2 misfires on cylinder 3. In the past it could get as high as 20. Now it gets a few misfires when idle surges a bit on warm restart, but then idles and drives fine. One other thing I noticed also post clearing adaptations is that I don't get the lack of power/sluggishness at lower rpms after the car is properly warmed up like in original post (pre clearing adaptations). So I think it's getting better but not quite there yet.

I'll maybe try to reset adaptations again, check fuel pressure, vacuum leaks, maybe get a new MAF to rule that out since that is tricky to diagnose. Other than that, not sure.

Other ideas to diagnose and check out are welcome .
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Discussing E46 M3 misfires and stumbles at low rpm, no codes in the E46 M3 (2001-2006) Forum - Engine: S54 - Max Hp: 333 hp at 7,900 rpm / 262 lb/ft at 4,900 rpm
Total Produced: 45,000+ - Years Produced: 2001 to 2006. at BMW M3 Forum.com (E30 M3 | E36 M3 | E46 M3 | E92 M3 | F80/X)