Engine Swap Experts Please Help - 00 GSR ECU not compatible w/ 98 GSR Plug Wires!!!!

I bought a 1998 GSR shell and a wrecked 2000 GSR with the motor. I pulled the motor and tranny from the 2000 with no problems. I go to pull the 00 GSR ECU and swap it over to the 98 GSR shell and the ECU does not fit the 98 GSR plugs. Out of the 3 plugs, the 2 outer plugs fit but the middle one does not. I double checked that both cars are GSR models and they are. Is there any easy way to swap the entire wire harnesses over to the 98 GSR (from what i can see it seemed pretty tough)? Any ideas? Thanks guys!