I'd peek under the fuel tank at ALL fuel lines, vacuum lines etc for any cracking / leaks. Your symptoms are very odd.
You may want to remove the tank while it's up and drain it looking for crap /water in the fuel . Bikes stored W/O a full tank tends to rust inside the tank and the fuel pump filter gets clogged eventually leading to failure. You may want to loosen the fuel pump 9tank off the bike) and see if any rust particles come out. If so, you'll need to remove the pump and dig much deeper.
I personally use Yamaha's RingFree(fuel system and top end cleaner) and "Gas Shok" (stabilizer) in every machine I own, (cage car, yard machines, etc).
The RF is NOT cheap but works wonders in fuel systems. I just used it this am in an "Echo" (commercial) edger that barely ran. Put a large dose of it in the tank (fresh gas), running at WOT, RPM's rose from approx. 5K to OVER 10,000 RPMs. It flushed out any crap left in carb plus loosens up carbons, etc in the top end.. It goes in ALL my customers machines.