I fixed it! Yay!
The problem: A dirty ignition/sidestand relay(This is the block with 6 wires going into it under the seat). None of the wires going to it appeared to be loose, so I think it was just dirty. I sprayed it liberally with WD-40. I'm going to keep an eye on it for a while but everything is working fine.
Thanks Andy and Klay!
Unfortionately, I made a stupid mistake as I was putting everything back together. When I installed the Yamaha Raptor Petcock on the gas tank a few months ago, I bent back the lip on the bottom of the tank to permit the free movement of the valve. Since then I've wanted to try and trim it off. So today, I bend it back and forth a few times and it pops off, great, everything is good. Wrong. I had no idea this was a seam for the gas tank. Now the tank is gushing gas from the seam if I try to fill it. I drained the tank and hung it upside down so that the gas will evaporate from the tank so I can take it to a welder tomorrow morning. Tomorrow I gotta hit the yellow pages trying to find a local place that will take care of it. Ugh. :( I'm an idiot. As much as I like the Yamaha Petcock, I don't think it was worth all this trouble. What I SHOULD have done was just carefully grind down a small bit of the lip.
Any suggestions on what sort of places would fix this for me? All I need is someone to weld this small seam back together. I'm guessing it's like a 5 minute job or less....
Curse my stupidity . ;) At least I fixed my electrical problem. Yay for persistance. :)