Sounds like a good question for the PCM/Engine swap guru Allen Nelson aka Farmtruc. Send him a PM or call NelsonPerformance and they can lead you down the right path. I believe you can just swap your truck harness, intake, accessories, oil pan and other goodies over to make it work. I don't think the 04 GTO had the 52x reluctor wheel so you should be good to use the truck PCM to run that engine.