01'WS6

I have a 01 WS6 and i just recently swapped my 6 speed for a 4l60e. I traded the wiring harness out of a 2000 SS harness. Ever since the swap i have been getting a TPS, EGR, and a rear o2 no activity code. I took the computer and had the computer flashed to an a4 and then i went to get the car tuned. The EGR and rear o2's were deleted but are still popping up after the tune. The tuner double checked it and said they were all deleted and now i cant seem to find the problem. Its a cam only car with bolt ons and a 3800 fuddle stall. Could it possibly be a bad ground? I checked the grounds on the back of the driver side head and they are good. Anybody have any insight on what the problem could be?

01'WS6

Any ideas?