your problem seems to be in the idle circuit of the carb ,you didn't drain the carb? or use Sta-bil in the gas? if the carb sat with fuel in the bowl ,  you most likely have a plugged/dirty pilot jet .but it may be a good idea to clean the bowl and main jet as well.

Mine used to stall also, until I raised the idle speed a bit, no more stalling.

Order a manual Yamaha Raptor petcock and get rid of that stock POS before you do anything else. Mine is a 2012, and that stock petcock went wonky at around 1200 miles. At idle, your engine isn't generating enough vacuum to keep it open, especially if you have been running E10 with no stabilizer, and the rubber gasket has stiffened up. Knowing what I do about the otherwise bulletproof reliability of this bike, I would not start tearing anything apart, potentially causing more problems, until I addressed the petcock first. You can try switching to "PRI" while running, then switch back to "RUN" while turned off. See if that works first.