01-04 engine With t-45?
 

I have a 98 gt with the stock tranny Could I throw a 01-04 in with the 98 harness and have everything work properly?
thanks

Absolutely. It will run fine with the stock NPI tune, but when you have the money for a proper tune it will run even better. The engine is a direct no BS swap regardless of your transmission, although you will retain your stock ignition/coil setup vs the PI engine's coil-on-plug. You can use your current 10.5" flywheel or keep the 11" flywheel that will be on the '01+ engine (unless obviously it has a flexplate instead of flywheel).