I'm pretty sure you'd find some differences in the grounds etc at the pcm or the main connector at the firewall. Gosh this post sounds familiar...didn't you post this same thing recently?
If I were in your shoes, I would swap the 2000 engine harness onto the motor and add the two wires for the boost control soleniod, then change the connector and extend the wiring for the map sensor. You have the wiring/connectors on the 98 harness. Then have someone load a 2000 GTP bin to your 2000 pcm and you are all set.
