Northstar help

I am new to the forum and would like to ask some questions regarding the 4.6 Northstar. I have recently finished a 5 year project building a Lamborghin Diablo roadster replica (www.lambobuilder.com) with a Northstar. The Northstar is a new 97. Because I couldn't hook up all the body sensors, I had to change out the computer and wiring harness to a 95 including a 95 throttle body. When the car runs for a while it begins to idle up and down and becomes very slugish. If I leave it in neutral and rev it to 3500 for a minute it then begins to run OK. the temp runs around 180 as I have two 4 core radiators cooling it. I only have about 250 miles on the engine. I am also looking for a good diagnostic software program for a laptop that may help me diagnose the problem.
Any suggestions would be appreciated.

Lambobuilder