I've had this thing for 10 years and have been just puttering around on it. It just turned 1500 miles so I de-carbonized it and put new tires on it. I also took some liberties with the muffler to get that cool sound.
First, I am not sure how the turn signal flasher gets wired in the battery box. I've tried tracking the wiring with my digital meter with no luck. The only manual I can find is the one here and there's some differences in the wiring diagram and the physical unit.
Unless someone took out the entire wiring harness and rewired it, these are the stock wires:
Clear insulator, runs to turn signal switch on handlebar. Bayonet connector termination. I assume that this is the common wire for the signals
White with bayonet connector, connected to green/yellow stripe, bayonet termination.
Brown with inline connector and bayonet connector.
The second issue is wiring the battery. There's those three wires in the battery box and that's it. I assume that one is positive and one ground but I'll be darned if I can noodle them out.
That and the rectifier on the ignition switch appears to be connected all wrong; all the outputs in the wiring are AC, which would make the battery connection iffy.