I vote for a lack of synchronization of the carbs. Any midadjustment is exagerated by the slack in the drive train, especially at idle.
It could also be crudded up carbs -- in particular the idle jets, which are the smallest jets in them.
Try synchronization first, then if that doesn't help try cleaning the carbs as follows:
Drain the float bowls completely with the fuel line to the petcock disconnected to get all the fuel out. Then close the drain screws and fill the carbs and fuel line with Chevron Techron Fuel System Cleaner. Using a baby ear syringe works well for this. Let them sit overnight and drain again -- with the fuel line disconnected.
Reconnect the fuel line and use PRIME position of the petcock to fill the carbs -- start her up and go for a ride.
I've used this technique on quite a few bikes and it works well.
Yamaha makes a carb cleaner with sometwhat similar instructions on the can, except they recommend diluting the solution with gasoline. With Techron I've never had any problems with carb parts being damaged in any way. It works and might with the Yamaha stuff too -- I've only used Techron.