[MotoMike]

... I repaired the wires and checked the fuses and battery (12.7V). All looks good, but the bike won't start. Nothing turns on when I switch the key to "On".

Does anyone have any idea what may have happened? Is there a fuse for ignition I haven't found yet? Something else that may have fried? I assume twisting the red to black damaged something....

Basically, when the thief bypassed the ignition switch by cutting and jumping the black & red wires together, that had the same result as turning the ignition switch to the "on" position. When they turned the engine off using the kill switch on the handle bar, the rest of the electrical system would have still been powered up, as if the key had been left in the "on" position, and as a result would have eventually discharged the battery. So despite that you've repaired the wires going to the ignition switch, I'm pretty sure your battery is now dead. Put the battery on a 2 amp charger and see if it takes a charge. If not, get a new battery.

 

[MotoMike]

I am not sure about this but I think if the steering is locked the bike can not be started. Was your steering locked?

The handle bar lock is a mechanical system, and is not interconnected to the electrical aspect of the ignition switch.