Using an OBDI computer on an OBDII engine is not uncommon. I've recently installed a '7730 ECM on a 1999 Vortec 454, I modified the .bin a 7.4 instead of a 5.7 liter. I'm thinking your going to do something similar to your ECM, modify the .bin for a 3.8 liter. The option of GMTuners is an affordable option to get a baseline .bin and get the engine running.

dave w