Well I have eliminated the battery as the cause of my no-start. Went over to the garage last night to start poking around with the bike, and it fired right up. Ran it for a few min, turned it off, then started right back up.
This point I went out for about a 15-20 min ride, to get the bike warm. Get back to the garage, turn it off, bike will not start. I went to take the key out and noticed the key was warm....very warm. Touched the cover that goes over the coil and ignition and burned my hand it was so hot. Im thinking that probably has something to do with it not starting! I am going to check all the wiring again today see what that turns up.
I bought the bike out in Rhode Island, and I live in CT, so it wont be any major issues with carb settings that way. The previous owner did not take care of this bike at all, and the more I look into it, seems he did not really know what he was doing. I do have a hyper charger on the bike and Short Shot V&H pipes (which he took the baffles out so it pops like crazy as soon as I get off the gas). I do not know if the carb was ever set for the extra air coming in and out with the mods. That could lead to my lean problem as well I would think. As for my coil problem, go figure, he told me he just did replace the coil as well.
I hope I can have some more answers for you tonight after I look into it a little more.
Thanks again.