I yout just swaping the motor, you will not need to use the 97 PCM, you just hook everything up the way it was in the 99 and run the 99's pcm. The motors are the same so it pretty much plug and play.
The only thing that is really differernt is the alternator bracket and vacuum lines off the supercharger. There may be a few other small odds and ends that a smidge different, but its shouldnt be an issue when your only swapping motors.