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Your 4L60E has a different TCC strat than the newer ones is all, I think it's lacking a 3/2 solenoid also. It may or may not work as the newer 4L60E's use this Ec3 stuff I believe it's called.
The '99 PCM will work better or you're going to have some strange lights come up with a newer one. Ask 99silver5.3 about this. BTW... '99 PCMs suck. I owned a '99 Z71 before my '01 and it was bad. '99s are also plagued by false knock from the PCM.
Your '99 has smaller injectors and a slighty different cam grind than the '00+ motors. So it will be down on power too.
The '99 PCM will work better or you're going to have some strange lights come up with a newer one. Ask 99silver5.3 about this. BTW... '99 PCMs suck. I owned a '99 Z71 before my '01 and it was bad. '99s are also plagued by false knock from the PCM.
Your '99 has smaller injectors and a slighty different cam grind than the '00+ motors. So it will be down on power too.