Can you help me with my four wheeler?

I have a 2005 Yamaha Raptor 350 SE,it wouldn't stay ideling an it shutoff when i pressed the gas,i finally got it to stay started i took the carb bowl off not really a lot of gew or anything i took the gas tank off drained it an put new gas in now it runs alright,,but it shuts off a couple of times starts back up though what could that be?and in where the carb is sometimes i press the gas it makes like a breathing noise sounds like it wants to shut off while pressing the gas but it doesn't,,and the main pipe where it runs to the header to the muffler gets really hot but the motor and muffler are only warm and how can i tell if the pipes or motor is able to get air or breathe right?