05 Mustang GT Random Misfire

[RedRoush3v]

I recently blew up my manual 05 mustang gt engine and swapped in a 09 gt engine(90k miles) keeping the 05 trans and pcm. Since install the car has had this weird subtle misfire i cant seem to resolve. Some other symptoms are sometimes when holding at rpms above 2000 for more than a couple seconds, the rpms will drop at which point ill left off the throttle and the car will misfire like its down a cylinder but 5-10 seconds later it will go back to normal idle. This has only been throwing ignition coil codes typically being P0354, P0356, and P0357(Circuit issues) and when i switch coils around, the codes dont follow the coils but typically wont remain on the same cylinder. There is also constant exhaust popping when holding at any rpm. Using HP tuners i can watch the fuel trims and they seem significantly off with the Ltfts jumping as high as 10 and stfts going as high as 18 under throttle. All the spark plugs look the healthy and so do piston heads. And the car is entirely stock other than a cold air intake atm. I've done the following:
-Spark plug changes
-Ignition coil changes
-Compression tested all good
-Redid timing and inspected valvetrain
-Voltage is +13.5 at all times
-Grounds are good
-Fuel pump
-Fuel injectors
-Fuel filter
-Fuel pressure sensor
-Retune
I also sent the pcm in for repair thinking that could be the only thing, they said it tested faulty and they fixed it but when i tried it again i had the exact same issues. Im pretty stuck and just want my car running again but dont want to take it to a shop lol. Any advice helps, thanks!

 

[86GT351]

Was a proper crank relearn done after the engine swap?
To perform a crank relearn on a 2005 Mustang, you will need an OBD-II scan tool or tuning device and must follow specific conditions: the engine must be at operating temperature (above 180°F/82°C), the vehicle must be in neutral with the parking brake applied, and you'll need to access the "Crank Relearn" or "Special Functions" menu on the device. The procedure involves following on-screen prompts, which typically require you to briefly rev the engine to a specific RPM (around 4500 RPM) and then let it return to idle.

Why a Crank Relearn Is Necessary

• After Mechanical Work: A relearn is essential after work on the engine, transmission, or clutch, which could disturb the timing correlation between the crankshaft and camshaft sensors.
• Symptom Correction: Failing to perform the relearn can lead to a recurring check engine light (CEL) with a misfire code, inaccurate misfire detection, or incorrect cylinder misfire reporting.
• Emissions Failure: The vehicle may fail emissions tests if the misfire monitor is incomplete.

THis needs to be done with a scanner or Hand held tuner. This should be done to verify it was completed. If that does not solve the issue, let us know.

 

[JC SSP]

Great info which should be pinned for future use.

 

[DieHarder]

Did you replace the coils or just move them around? Reason I ask is the original coils are old and the pig tails tend to lose elasticity where they wont make a good connection anymore with the top of the plugs. The car will idle fine but can exhibit random misfires at idle and/or under load. Good news is OEM coils are available on feebay for less than you might think. Since you replaced the engine with an '09 you'll have to determine if you have black (05 - 07) or gray boots (08 - 10?).

Black -

Pardon Our Interruption...

Gray - https://www.ebay.com/itm/3968352734...mphSUZyJkGsUntDvAolyBBklg=|tkp:Bk9SR_CghfSaZg

 

[RedRoush3v]

Was a proper crank relearn done after the engine swap?
To perform a crank relearn on a 2005 Mustang, you will need an OBD-II scan tool or tuning device and must follow specific conditions: the engine must be at operating temperature (above 180°F/82°C), the vehicle must be in neutral with the parking brake applied, and you'll need to access the "Crank Relearn" or "Special Functions" menu on the device. The procedure involves following on-screen prompts, which typically require you to briefly rev the engine to a specific RPM (around 4500 RPM) and then let it return to idle.

Why a Crank Relearn Is Necessary

• After Mechanical Work: A relearn is essential after work on the engine, transmission, or clutch, which could disturb the timing correlation between the crankshaft and camshaft sensors.
• Symptom Correction: Failing to perform the relearn can lead to a recurring check engine light (CEL) with a misfire code, inaccurate misfire detection, or incorrect cylinder misfire reporting.
• Emissions Failure: The vehicle may fail emissions tests if the misfire monitor is incomplete.

THis needs to be done with a scanner or Hand held tuner. This should be done to verify it was completed. If that does not solve the issue, let us know.

I did some research and contacted some shops and i am under the impression that the 05-10 mustang GTs dont have a crank relearn feature. If this is wrong please let me know.

 

[RedRoush3v]

Did you replace the coils or just move them around? Reason I ask is the original coils are old and the pig tails tend to lose elasticity where they wont make a good connection anymore with the top of the plugs. The car will idle fine but can exhibit random misfires at idle and/or under load. Good news is OEM coils are available on feebay for less than you might think. Since you replaced the engine with an '09 you'll have to determine if you have black (05 - 07) or gray boots (08 - 10?).

Black -

Pardon Our Interruption...

Gray - https://www.ebay.com/itm/396835273471?fits=Year:2009|Model:Mustang&_skw=09+Mustang+coils&itmmeta=01K3BM1A17NYCDV0KFAB0BDVQD&hash=item5c6539baff:g:5bMAAOSwunpoU5Qn&itmprp=enc:AQAKAAAA0FkggFvd1GGDu0w3yXCmi1eOq+WX5GLL5iGfdtNssE9fIh63SRCoxXvl/sVrhgoholPERmdtwhF3iLjWFrgPQYAbhZesnEuXzoq2+rqFx8FfgkuD0+M8UzeUE8TrA3nvcpkFYBtT0x69Dv9hPxoWApeu4e+jjP9N6BViptXf1Z2JxtJdQWLwM6oniJCpTJyNupdkmQStEJK0Jw7dzxvctkN9EgNCUFg4gfV4foVt89mqGvUuvvY0k5aoOGm28JmphSUZyJkGsUntDvAolyBBklg=|tkp:Bk9SR_CghfSaZg

I had an extra set of coils that i bought used a while back. Than i also had the stock ones from my 05 engine that never gave me issues. Ive swapped them out, moved them around, applied dielectric grease, and i cant seem to find a consistent issue with them. Both sets are black and i think are for 05-07 engines but i did some research and it said that although they did switch their styles through the years, they work identical and should be interchangeable. Again, if this is wrong please let me know

 

[RedRoush3v]

In addition to what ive mentioned, the car seems to opperate way better under load. Not dropping in rpms and doesnt even really feel like its down any power, but the exhuast popping is still there. Fuel trims are still off under load and it doesnt seem to be till the car is under significant load or WOT that it will throw the code for ignition coil circuit. Now im not to sure how consistent this is as im trying to avoid driving the car as much as possible but figured id throw it out there as it was something i noticed.

 

[86GT351]

I did some research and contacted some shops and i am under the impression that the 05-10 mustang GTs dont have a crank relearn feature. If this is wrong please let me know.

Do it anyhow. Can't hurt. I work for FOrd and I can tell you we do it on all cars with these repairs weather needed or not.

 

[RedRoush3v]

Do it anyhow. Can't hurt. I work for FOrd and I can tell you we do it on all cars with these repairs weather needed or not.

I contacted my local dealership and they said they cant do that. I also called two local shops who said that wasnt something they think could be done and unfortunately i dont have the kinda scanner to allow me to even view that option let alone preform it. Using my handheld im able to preform a KAM reset but nothing else

 

[86GT351]

I contacted my local dealership and they said they cant do that. I also called two local shops who said that wasnt something they think could be done and unfortunately i dont have the kinda scanner to allow me to even view that option let alone preform it. Using my handheld im able to preform a KAM reset but nothing else

Then call another dealer. Can't makes no sense. It can be done. Sounds more like they don't want to.

 

[RedRoush3v]

Okay ur right, its weird how many times i had to call the dealership before i got someone who actually knew what i was talking about lol. Ill let you know what that does, thanks for ur quick responses and knowledge.

 

[Frankydanks]

Have you found issue?

 

[RedRoush3v]

No, I haven’t found anyone to preform this crank relearn feature mentioned previously and haven’t had the time to just take it in for a diagnosis yet. Ive done more troubleshooting but still haven’t found anything. In addition to what i mentioned before, when stationary the engine is also increasing in rpm when holding throttle position steady, and sometimes decreasing. But when under load and driving, the car drives just fine(atleast under 3500rpms which is as far as ive taken it) I tested pressure leakage thinking maybe a valve was burnt but all cylinders displayed within 90%. Ill take it in for a diagnosis when I have a chance and update the forum

 

[Pentalab]

Was a proper crank relearn done after the engine swap?
To perform a crank relearn on a 2005 Mustang, you will need an OBD-II scan tool or tuning device and must follow specific conditions: the engine must be at operating temperature (above 180°F/82°C), the vehicle must be in neutral with the parking brake applied, and you'll need to access the "Crank Relearn" or "Special Functions" menu on the device. The procedure involves following on-screen prompts, which typically require you to briefly rev the engine to a specific RPM (around 4500 RPM) and then let it return to idle.

Why a Crank Relearn Is Necessary

• After Mechanical Work: A relearn is essential after work on the engine, transmission, or clutch, which could disturb the timing correlation between the crankshaft and camshaft sensors.
• Symptom Correction: Failing to perform the relearn can lead to a recurring check engine light (CEL) with a misfire code, inaccurate misfire detection, or incorrect cylinder misfire reporting.
• Emissions Failure: The vehicle may fail emissions tests if the misfire monitor is incomplete.

THis needs to be done with a scanner or Hand held tuner. This should be done to verify it was completed. If that does not solve the issue, let us know.

Can he do it himself...assuming he has a hand held tuner or scanner?
Can it be done with a SCT-X3 handheld tuner ?

 

[RedRoush3v]

I have the sct-x3 and it wouldnt allow me to do it. I also have the mpv3 hp tuner and it wouldnt allow me to do it there either. I took it to a speed shop in the area and they tried but couldnt do it on any of there scanners either.

 

[86GT351]

I have the sct-x3 and it wouldnt allow me to do it. I also have the mpv3 hp tuner and it wouldnt allow me to do it there either. I took it to a speed shop in the area and they tried but couldnt do it on any of there scanners either.

So then that would lead me to believe there is an issue with the vehicle. If the device being used shows the feature but won't allow it, something is stopping it from working.

 

[RedRoush3v]

It doesnt show the feature tho thats the thing. None of the devices did. Only a KAM reset which ive done a couple times.

 

[StockishS197]

It doesnt show the feature tho thats the thing. None of the devices did. Only a KAM reset which ive done a couple times.

I have never seen a crank relearn on a 3v with a SCT device. Also never performed a crank relearn after changed clutches, etc and never had the problem you are describing.

The brown coil boots for the revised 3v heads are narrower and longer than the 05-07 plugs. I would try getting replacement brown boots for the 08-09 and see if that solves your problem. The coil itself should be interchangeable.

Edit, because I have to ask….you did put the revised 08-09 spark plugs in and NOT the old 2 piece plugs, correct?

 

[RedRoush3v]

Yeah i have the 12mm spark plugs for the 08-10. The car is at a shop rn so im waiting to hear back from them. Maybe your right on the coils, ill update the forum when i hear back from the shop.

 

[RedRoush3v]

The shop told me that there is a difference in the engines from 05-07 and 08-09 in regards to the crank sprocket and tune. They told me id have to get the ecu reseated but all the research i do says otherwise. Seems like it should be a straight forward swap with the only differences being spark plugs and coil boots. All i can do now is try the 08-09 coil boots and hope that does something. If anybody has any ideas please let me know.