02CamaroZ1985

I have a 2002 Camaro Z28 that I did a 6 speed swap on and my service engine soon light is on and the codes that it’s throwing all has to do with the automatic being gone. Do I need to switch the computer out for a manual pcm or can I have my current pcm which is programmed for the automatic reflashed to recognize it's a 6 speed now? I’ve been told that my current pcm has a transmission control unit and the 6 speed pcms don’t. Does that matter or can I have it reflashed to bypass the transmission control unit and recognize it’s a 6 speed? Also I was told that I might have to switch the pins on the pcm. If I can reflash my current pcm which tuning software is the best to do that with for an LS1? Any help would be greatly appreciated!!