The tune from the previous engine should have just worked (at least somewhat) with the new one. The ECM holds the tune, not the engine. I presume it ran well enough originally before all this stupid stuff started happening. It sounds like there has been more than just mechanical hackery here if it runs as bad as you say. I concur on just finding a decent 4.0 and putting that in. You are really getting in deep with custom everything to put a V10 in there, for example.