Irvinmac3

hello everybody. i am working on 2 cars at the moment. car 1 is a 1998 camaro ss z28. the car was an automatic with an ls1. car number 2 is a 1999 camaro that had and ls1 t56 combo. I am taking the 1999 computer and putting it into the 1998 car. as most of you may already know my problem, the 1998 wiring harness has 3 connectors under the dashboard, as the 1999 has 2. so my question is, what all do i have to do to make the 1999 harness work in the 1998 car and what to i have to do to make the 1998 auto harness work in the 1999. im doing this swap because the car im building was an automatic and i bought a convertible car with a good 6 speed in it. i have seen a few forums that mentioned re-pinning the harness. i tried reading, and rereading them but i dont quite understand what wires im suppose to be moving and where to move them too. if anyone could guide me in the right direction or give an kind of advise that would be greatly appriciated. thanks, Irvin.