Reprogramming a PCM (ECM) will NOT fix it, if its suffered damaged from a short, only replacing it will fix the damage.
In my '99 Neon R/T, I had a short in the wiring for one of the injectors, kept blowing the fuse for the PCM/Fuel Pump. It left me stranded 200 miles from home, I had mis-fire codes and a fuel injector circuit code. I decided to risk it and put in a bigger fuse (yes, the thing they say never to do) and it kep the motor running without blowing. When I fixed the short, I still had the same problem, this time with codes for "Fuel Injector Driver" that is a part of the PCM.
Sure enough, using the bigger fuse let the short fry the part of the PCM that does the amplifying/driving of the fuel injector circuit. Since I had put an aftermarket PCM in my Neon R/T, I still had the OEM PCM on the shelf, put it in and it ran just fine. It was one part of the PCM that was fried.
BUT, I had codes for "Fuel Injector Driver", NOT just symptoms of something on the engine NOT working right. There are a lot of people that waste money on new PCM's/ECM's because they jump to conclusions and assume the PCM went bad. Good luck, I don't know of any test for the drivers on the PCM that wouldn't involve something like a ocilliscope, hopefully there is some test out there to confirm it.
And sadly, with the Anti-Theft Measures, I don't think you can replace the PCM yourself, the dealer starscan tool is required to program it for you vehicle and enable it. I don't think it will start or drive, until you get it to the dealer, meaning you likely have to pay them to replace it as well, they won't let you do it in their parking lot and bring the tool out into the parking lot. (That is one that has some justification, I will continue to rant about the others that have no justification to pull this kind of crap).
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