03 Bonneville Motor in 85 fiero Passkey issues

Hello, I'm having a bit of an issue with my fiero that I'm having trouble figuring out. I was unable to turn off passkey in hptuners on the 2003 pcm despite setting VATS to pwm and turning off 1626,29,30,31. When I plug in my spare 99 gtp pcm the car runs but won't shift into 3rd. The guy who built.my harness said he wired the harness so it can he used for any year transmission, but from what he knows the pcm year needs to match the transmission year. I can tune both the 99 and the 03 pcm. I did try to overwrite the tune completely on the 03 pcm, but the car still just cranks and won't start.