I wish I could help with the wiring...I only had the engine and computer harness, and I'm not sure how much of it ties into the bike's wiring system, trip computer, cruise control, etc... I would try leaving everything electrical in place, except for the injector harness. I believe the LTD ignition timing curve is based on many of the sensor inputs...air & coolant temps, manifold vacuum, RPM and throttle position. If you use the Aspy wiring, you'll probably lose cruise control and trip computer functions...hard to say what will and will not work. Sounds like a fun project!
Are you having issues with the FI system? It's awesome when it's working properly!