I'm currently in the middle of doing the 16bit to 32bit ECU/Rotor swap on my 2000. The instructions contained in this thread are great but can be confusing when it comes to the pin swaps and moves...primarily because the instructions show the 32bit pin out and from the ECU connector as far as numbering. Well, you're not working on a 32bit ECU, you're working on the harness ECU plugs on a 16bit machine. So, I've attached something that I hope will clear up any confusion for anyone attempting to do this mod.
This picture represents what you are looking when you have just removed the plugs that were attached to your 16bit ECU:
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