Update to 2000 to 2004 3800 SII engine swap incompatibility:
Finished my engine swap just in time to make it to a glacier travel and crevasse rescue course in British Columbia. Everyone loves this Bonny and I got respect with my engine story. Ran great the whole 1200 mile trip except for the Service Engine Soon light being on. Passed by a shop in Golden BC with mechanics lounging around, so I pulled in, told the engine swap story and asked if they had time to pull the codes. Sure, and it was no charge!
Turned out to be the upstream oxygen sensor. Of course I had kept the 2004 sensor. Went back to that cursed 2000 engine, pulled the sensor and compared resistance readings. Only two pins out of four give any reading and they were very different:
2000: AC delco with slits: 4 ohms
2004: Delphi with holes: 10 ohms
Swapped the 2000 sensor to the 2004 engine (connected to the 2000 PCM), disconnected the battery an hour (15 minutes is not long enough to reset the PCM) and all is well! Checked Partszone and they have vastly different prices for the '00 - '03 upstream oxygen sensors ($74.93) compared to the '04 - '05 ones ($31.89). Probably NOT compatible for the older PCM.
In summary for the record:
2000 to 2004 3800 SII engine swap incompatibilities:
-Fuel injectors. '00, '01 - '03, '04 - '05 different wire plugs
-Upstream oxygen sensor. '00 - '03, '04 - '05 different sensor characteristics