Quote Originally Posted by bluegtp91 View Post
'03 Transmission WILL NOT work with a '99 file, Scott.

Been there, done that.

Just get a '03 GTP PCM, toss the '97 motor in, and put the gear settings to match the N/A transmission, done and done.
I clearly said that he should put the 97 trans in with it....

I have tried to run a 03 3.29 trans boosted setup plenty of times with nothing but issues each go. Can it work, sure, but if you want simple, just toss the 97 trans in and leave your 03 around for a spare or sell it.