Thanks tegboi.
Got a new plan. It's a slight backwards step, but will be better in the long run. The bike is currently running MC16 electrics, including the flywheel generator and ignition pickups. This is less than ideal for my MC18 motor, which I assume has slightly different ignition timing and RC valve timing, since Honda changed virtually everything between models. The biggest difference is the lack of a PGM controller on the 16. The PGM unit controls the RC valves, ignition maps, and air correction solenoids. I'm currently running the MC18 carbs with the air correction circuit blocked off.
I will be swapping the entire wiring loom and flywheel components for MC18 parts from the spare bike. This seems like the smart thing to do. I'm sure the bike will be easier to set up and certainly perform better if everything was MC18.