There is a major valve body difference in the middle of 99 as well. The PC solenoid operation changed, as well as the valvebody.
I have never had a "post 99" valvebody (aka valvebody B) work correctly on a 97-98pcm/bin file.... I also have had issues running 00+ pcm's on 97-early99 transmissions.
You can typically tell valvebody differences by looking at the transmission fittings, but it is not always a perfect tell... Obviously the push in fittings will be the later style valvebody.