What is your idle speed? (bike fully warmed up, sitting at a stop in neutral, hand off of the throttle). If it's 1000 rpm or lower, it would run quite rough. Try adjusting it closer to 1500 rpm, and that might fix part of the issue. (to adjust it, there is a black knob to turn down by your left knee peeking out near the side plate of the bike.)
Edit: I owe KKim yet another beer...
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