I just had an engine fire and melted half my harness. The engine harness is not bad at all to change out, just be careful and watch for ground straps. Everything else is pretty much plug and play since all the pig tails go in their own places and used harnesses pretty much fall into place. With that said, I have found these harnesses to be car and year specific. I had to go here to find my harness and after three (the places I contacted gave me the VIN of the car the harnesses were pulled from and I called my local GM dealer to confirm which was correct for my car based on VIN) I found the perfect one. All the pins matched up and it was perfect. LINK ------> Car-Part.com--Used Auto Parts Market

Regarding your problem, I agree with Bill. Someone put the GTP motor in your GT car and that's it. I bet you are still running your GT harness and PCM. How does the car shift while driving? Does it shift weird or smooth? The GT vs GTP transmissions are different as well. Gearing difference calls for different shift points between the GT and GTP PCM's causing the transmission to shift weird. The reason I ask this is because would buying a used PCM help, or would it be better for him to figure out what he has first then go to Intense or Overkill and have a custom tune done for his specific application? He'll have to have his "new" PCM flashed anyway for his VIN and such if he has emission testing?? I dunno, just a random thought.

I would start out with a new harness. I bought mine for $100 ($75 for the harness and $25 shipping from OH to TN) Search that site and you'll find a good deal.