PCM and Emissions

I cant seem to find any info on emissions standards in Georgia with regards to PCM change. I want to put a 5 speed in since my auto is going. Now i have a programmer (superchips Cortex) which is supposedly capable of flashing the auto PCM to function with the manual with no codes or limp mode. Anyone ever gotten this to work? It always asks me when i flash if the truck is manual so I'm assuming it does have this capability even though it reads my auto (to scared to flash it that way and see i need the auto to work for a while longer). Also if it doesn't and i do swap the PCM to a manual PCM will the different vin in the PCM cause an automatic emissions fail? ANy info is appreciated.

Thanks,
Chris