Please Help!!! Gradual engine rebuild?

[Rice Hunter]

Hey guys. My friend is looking to do some upgrades to his 94 GT. It has 100,000 miles on it but it runs very well (it used to be mine ). A plan developed to slowly replace the engine part by part, and slowly increase the power as well. He was thinking about replacing the heads first. I was wondering if there is any issue with changing the set up of the motor without changing other things such as the chip etc. Can a swap like that be done easily? Will it improve horsepower well if he got a good performance brand? I have no engine experience myself and he has some (mostly a late 60's corvette). I am looking to learn as much as I can. If you can give any help or experiences with a gradual engine rebuild please do!!!!!