im no wiz at this, in fact im still learning a lot, but my idle always seemed to run a little lean. so i turned it out 1/4 more than factory settings and it runs good. do i have it properly tuned? probably not, but my header has never glowed on me and my spark plug looks golden brown like it should so im satisfied until the mods start pouring in. i would just tinker with it until it runs well. once you throw a slip on or start doing mods factory settings are going to be less important. plus elevation has a lot to do with jetting because of how thin or thick the air is. with the information i have i would guess yamaha has to come up with a general medium with jetting for mass production. hence the air/fuel screw is on the outside of the carb to make adjustments on the fly.
if you think you have to make adjustments, do it when the bike is warm. it will run lean when its cold. and you shouldn't have to touch it after that until you start messing with the flow in other areas