do you ever adjust the choke after the bike warms up. I had the same problem, I f I adjust my choke to idle at 1.5 it goes away. UI let it warm up to 112 degrees at full idle after the warm up lower it to like 1.5 and it will stop.
Sometimes when I'm stopped and shift up to neutral (using positive neutral finder) the bike's neutral indicator flashes on then off again - but it is in neutral - if I let out the clutch, the light comes back on. Are you sure you're in second, or is the light just off? Try letting the clutch out slowly and seeing if you pull forward or if the light comes on...
when your at a light and in first gear, ease out the clutch slightly until you find the friction zone(it moves a little) then you can lightly shift in to neutral. in the msf they recomended you shift into neutral after the bike is off.
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