Ignition Problems

As my sig indicates, I have a heavily modified 2001 Mustang GT. After over 2 years of work on the build, I finally got the car running. Unfortunately, I am getting a ton of coil malfunction codes: p0354, p0355, p0356, p0357, and p0358. Needless to say, the car runs like crap, but I thought at first it was just the big cams, since it took a while for the codes to appear. I've ruled out bad coils as the culprit, so I'm thinking there's a wiring problem somewhere. Any ideas?
 
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If this were my car the 1st test I would do is to confirm a solid +12 volts on every COP and fuel injector with the key on.

Next I would confirm a firing pulse on the COP and Fuel injectors. A "noid" style test light is the best thing to use.

It wouldn't hurt to have the alternator tested for excessive AC ripple.

>>possible causes for P035x DTC's

Open or short in Ignition START/RUN circuit
Open coil driver circuit in harness
Coil driver circuit shorted to ground
Damaged coil
Damaged PCM
Coil driver circuit shorted to PWR
 
I finally got a chance to work on the Mustang tonight. I verified that each coil and injector is receiving +12v. I then put a noid light on the #5 coil, and got nothing when cranking. I'll test the other cylinders tomorrow when I can get a helper to turn the key while I watch the noid light. Given that I'm getting 12v at each coil but I'm having problems with an entire bank of cylinders, should I be looking for a new PCM?
 
No, chances of it being PCM related are slim, possible but slim. I have noticed when one coil goes bad other follow soon after. I had similar codes one time on F-150 and was reluctant to just start changes coils (COPs) but finally did and solved the problem, it has been working for over a year. Try buying a whole new set from say MSD or Accel. The OEMs are pricy and the part stores brands in general suck. I found MSDs to be the ticket. That is what I have on my KB GT and they even helped with spark blow out. A simple way to test your coils is to put a volt meter on it and check resistance, ohms. Not full proof but will give you an idea. I believe it to be 15 ohms but check a couple know working COPs and get a value, then check the suspects against it.
 
Is the whole driver side bank not lighting up to the noid test? It sounds like there could be a wiring issue if the whole bank is not firing, or the PCM is bad. Follow wmburns' walkthrough or PM him for more ideas..even if you clear the codes and reset the battery it still runs like crap?
 
I guess I should have mentioned that before I pulled out my multimeter and borrowed a noid light, I did the resistance test on all 8 coils, and they measured within spec. I then bought and installed 4 new Pep Boys coils, but nothing changed (I returned them after the test). At this point, I think I can safely rule out coil problems, so I'm looking at either an electrical fault or a bad PCM. Given that I'm missing the entire driver's side bank but they're getting +12v to the plug, I'm leaning towards a bad PCM.
 
Is the whole driver side bank not lighting up to the noid test? It sounds like there could be a wiring issue if the whole bank is not firing, or the PCM is bad. Follow wmburns' walkthrough or PM him for more ideas..even if you clear the codes and reset the battery it still runs like crap?
The car still runs like crap after clearing the codes and pulling the battery. I could only see the noid light from the driver's seat when it was connected to the #5 cylinder, so I'm going to have my fiancee help me out tonight with the rest of them. I'll also test the noid light on a working coil to make sure it works lol.
 
If it were mine a continuity test between the coil connectors and the connector at the PCM would next.

Check the wiring harness in behind the engine for damage. Maybe it was pinched or stressed when the engine was removed/installed.
 
I tested the injectors with a noid light and they all passed. I checked the coils, and cylinders 1,2,3, and 7 checked out, but I got nothing at 4, 5, 6, and 8. I would agree that a continuity test between the PCM and coils is the next logical step. Does anyone have a diagram of the PCM connectors so I know which pins to probe?
 
I have the 2001 factory service CD. The wiring diagram shows an inline connector between the PCM and spark coils 4,5,6, & 8 (there is a separate connector near the firewall for the other 4 coils). I am making a leap of faith that coil numbers and cylinder numbers match, but with Ford, who knows? It is a 16-pin connector and clipped to the body just below the mass airflow meter.
On my '03, I can see it if I look straight down between the passenger-side valve cover and airflow meter connector. There is a fat A/C hose running in that gap, and the connector is below it. Just follow the harness down from the front-most passenger-side coil and you will eventually come to the connector.
I would try to move that connector and harness with a stick to see if anything changes.
 
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For the 2001 Model year, connector C104 carries COP 1, 2, 3, and 7. Connector C1007 carries COP 4, 5, 6, and 8. So n0v8or is onto something. Great call!!

I may be able to help you get a full Ford service manual with wiring diagrams for your car. PM if interested. These would be a HUGE help tracing down a possible wiring problem. Having accurate wire colors, connector pins out with face diagrams will save you a ton of time.
 
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n0v8or, you were right. I looked for that connector near the MAF, and it wasn't connected to anything! I found the other half stuffed behind the engine. I can't believe I missed that when doing the engine swap. I feel like an idiot. Thanks guys for all your help. I just hope I didn't screw up the engine's break-in period by running it on half its cylinders for 30 miles.