I've read on the Dakota R/T forum that the guys that do manual trans swaps on '00(maybe '01) and later trucks have had more trouble getting the auto trans computer to work. Flyin Ryan Tuning is one of the few guys that has been able to tune these later trucks for a manual trans and not have a check engine light, or have the engine running in limp mode. They say the '99(maybe '00) and earlier R/Ts are easier to tune the auto function out of the computer.
I found a '98 Ram 5.9 manual computer for when I swap my '94 OBD1 harness to a '98 OBD2 harness in my Scamp.