All this working/not working happened as you played with the ignition switch and its wiring. That's at least some evidence that the problem lies in that area.
I don't think jumpering those two wires together damaged anything. When your ignition switch is working that's what it does - it shorts those two wires together in the "on" position - so you were just doing the switches job.
There is another pole on the ignition switch that shorts the other two wires together when the switch is in the "on" position. My wiring diagram from the anythingatv site is kind of hard to read. I think the two colors are Blue/Yellow and White/Black. These also have to be shorted together for the engine to run. What this half of the switch does is connect the output of the timing pickup coil in the stator (the signal that tells the ignition module to fire the spark now!) to the ignition module (through the remote control receiver). I'm thinking the ignition switch is broken up inside and it is hard to get both halves of the switch working simultaneously. Try jumpering both halves of the ignition switch and see what happens (blu/yel and wht/blk together, red and brown together). Its two and two - don't wire all four together - that will blow the fuse.
Also check the handlebar run/stop switch to make sure that is in the run position.
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