I've done the reverse in a Riviera. The only differences were that there were 5 wires added to 97 from 96. Being that the pcm and wiring all resides in the engine bay on the Bonnie and that you swapped everything 100%, all should be well.
Things you can check would be the firewall connector for any differences in ign0, ign1 and ign2 as some of those may be 5+ versus 12+. Other than that I would be checking the connector at the trans, the ground on the back of the block near the oil filter adapter and all wiring for any pinching or visual hints. Maybe dropping the pan to change the fluid/service the filter.
00 Regal GS: All kinds of cool stuff.