Here is what I have so far...
I have checked the stator for resistance (0.3 ohms) and AC output (40.2 VAC) and everything is perfect.
I leave the battery on the battery tender jr when its not being rode. If its not on the tender I get DTC b1006, b1007, and occosianlly the p0562.
The battery is 5 years old and haven't had an issue until a couple hundred miles ago which at first made me think the battery was going bad but I've never had a bad battery throw DTC. They usually just don't start.
When the stator is unplugged from the regulator the bike fires right up. When it is plugged in it has to crank a few times before it fires up.
I know the regulators are known to go bad on this model year and I believe it is the original at 13,300 miles.
I am going to have the battery checked at auto zone tomorrow.

What are your guys's thoughts?
I need to get this fixed before a take a 4 hour round trip to Indianapolis plus cruising around town for the Moto GP race next weekend.
Thanks guys!