I feel your frustration. My BMW F650 had those symptoms even though I had not touched the carbs. (Yes folks, carbs. A single-cylinder with (2) carbs, one for each intake valve. But I digress...)

The idle circuit of most carburetors is adjusted at the factory and then sealed, so I figured that if it had been running and now was not, there must be some problem other than being mis-adjusted.

I then hit on the idea that since I had not actually ridden the bike for some months, that the gasoline might be stale. I drained the tank and put in absolutely FRESH premium grade gasoline. I started it on "choke" and let it idle for some time to get really warm, then tried to ride it. It needed gentle throttle movements and occasionally sputtered and stumbled for a few miles, but the fresh gas with all of its volatile components intact burned better, and the premium with its load of detergents eventually dissolved and cleaned out the idle circuit jets.

My understanding now is that combustion was marginal after most of the more volatile and easily-ignited stuff had evaporated from the old gas in the tank and that some scum in the idle circuit was the last straw.

The bike has been running fine since, and I make sure to empty the tank regularly by riding often (whee!) and buying only premium.

So, if your Yamaha has been not running a long time, try fresh gas. It only takes about a gallon in your tank to prove one way or another, and might save you hours of frustration.