If you put the petcock on prime it may solve the problem. If it does, put a genuine Yamaha raptor petcock on it.
The stock petcock is prone to failure with baffling symptoms.
I took my brand new Suzuki petcock off and replaced it as soon as I got my bike. I knew that it would give me trouble sooner or later. Warranty be darned!
I think it still may be an adjustment or a plugged pilot jet. Anyway, you will sort it out or the entire site may have to commit suicide.