I believe most of the changes in wiring from the OBDI to OBDII setups are in the plugs that connect the harness to the ECU. One thing that is different is that you have two oxygen sensors with your OBDII setup but conceivably if you keep the same exhaust tract those will remain.

You may want to check out www.car-part.com. They're an online listing of salvage yards throughout the country, I can't imagine not being able to find a newer motor on that site.