Engine/Transmission (1998.5 - 2002) won't shift into o/d

[summitracer]

well we put the 2001 engine in the 99 truck and it has been a pain to get things working correctly we got a pcm which we thought was the right one this time and it seems to run real good but now it won't shift into overdrive it shifts perfect with the 99 pcm but won't rev past 2000 rpm without fooling the transmission into thinking it's in park now with the 2001 pcm it runs great but won't shift right any ideas?