I'd clean the carb properly and set the mixture screw according the the factory service manual as well as the idle set screw.
When I say clean it properly, I don't mean spraying it with carb cleaner. I mean tear it completely down, soak the parts in carb cleaner, then blow all of the passages and jets out with compressed air from multiple directions. Then just to be absolutely sure, spray carb cleaner into the passages and jets and blow them out again with compressed air.
Once you are absolutely certain that the carb is clean, put it back together according to the factory service manual, set everything to spec and use that as a baseline to tune the carb. Again going by the factory service manual recommendation for setup.
I'm guessing you don't have a factory service manual, so If I were you, I'd get one. Yamaha manuals are pretty easy to get ahold of if you are handy with Google.