Cleaning out the carb after sitting for a few months is always a good idea. Put some fresh gas in the tank and make sure the cap is venting so fuel isn’t held in the tank in a vacuum.
But, I think your problem is valve clearance. Your manual should explain how to check the clearance and how to shim them within specs. Plenty of info here as well under the maintenance section. If they’re even a little tighter than the limit, it will get harder to start when warm. It will start fine when cold if they are at the bottom of the limit, but once the valves warm up, they stretch enough to be out of limits.
94mm bbk, +4 stroker, Hot Cams, Vertex piston, FMF Power Bomb header and Power Core can, KW black diamond valves/dual springs, FCR39, K&N, Elka long-travel LT fronts and rear, Houser +3, +3/4 LT A-arms, American Star pro xs chromoly tie rods, Dyna non-programable, Tusk +3 axle.