So I took the fuel tank off...
I took the tank off to run a powerlet cable, put everything back together and the bike ran fine for 3 miles. Then it died when I came to a stop. I can get it to restart with no choke and the throttle held wide open, barely, but it won't stay running, it sounds awful and is blowing smoke out of the exhaust. It definitely smells flooded as well after restart attempts.
It is an an 09 with 960 miles, not even out of its break-in yet.
I am sure it is related to the tank removal, so what could it be?