Just curious... did your bike set all that time with ethanol-blended fuel? There might be some corrosion or deterioration in the fuel supply chain.
My '13 sat for a year before I bought it... I know the tank swelled, but in addition to that, it ran like crap until I finally made the switch to non-eth fuel. I would probably continue to run SeaFoam through it for a while, and see if you can source non-eth fuel for it. I have to run at least 90 octane in my 796 or it detonates, too, but don't get carried away... too much octane will make it run like crap.
2013 M796 ABS in Artic White
1993 XR650L (the Torque-a-Saurus)