What I would do:

Pull your motor, drop it into the GTP. Top swap from the GTP Motor onto yours. (Get fresh gaskets, and all that.)

Use the GTP Trans, ECU, ect...

You may want to re-cal the ECU for the higher compression you will get with the L36 Shortblock, but basically you'll end up with a stock GTP when your done. No wiring changes needed.

-Rob