Dad,
Thanks for the help on this one. Not quite sure (yet) where I've gone wrong, but I'll post up what I was attempting to do and maybe the errors can be worked out...
First, I can't see a short to ground, except maybe the alligator clip? I may have to insulate that some way, but I wanted it in place so that I could hook up a battery and provide power to the bike with out the engine needing to turn over. Mainly to use the oil pump to help drain the oil and to lube up the top end prior to starting, but also in case I needed a bit of juice to get things going (for some reason).
For the switched flasher, the idea behind that switch was to replace the ignition. Black wiring is switched +12V on Hondas and would normally be after the ignition switch, which I no longer have. Still look OK?
Finally, I am very interested in this one-wire idea of schematics, because I've spent a bit of time altering the harness to get rid of as much ground wiring as possible. I've just used the frame, instead. In that type of diagram, how do one represent a switched ground like I have for my headlight (switching the ground instead of the +12V allows me to turn off the high beam and the low beam at the same time)?