The 500, especially with a new top end, can be hard to start with an old kicker and jetting being off just a little. I had an old kicker and it was making my boot slip off. As soon as its out of square with the bike its tough to keep your boot on it. That led to tearing up my boots and also getting cracked on the leg a few times. Also, mine has always needed me to open the throttle a little when warm, (all the way open after a wreck) no throttle when cold. Sounds like an air screw or pilot may be off adjustment or partially clogged, or Maybe you are going a little overkill on feeding it fuel during prep. I haven't seen too many people lean it over, rock it and hit the gas with a few easy kicks and then still cracking the throttle with the choke on. Try it without any of the prep.
Try gas on, choke on, kick a few times easy, cycle to the compression spot, wind up the kicker to the highest spot, then drop the mojo on it. No throttle. It should start with a high idle, then calm down to a normal level, then thats when I turn off the choke.
After warm, 1/3 to 1/2 throttle, also needs to be at TDC to get a full kick.
Electrical problems suck, I hope you get it figured out, good luck.