Throttle shaft bushings. Try to wiggle the throttle shaft. Remove the throttle cable and see if there is any up and down play, if so you need a throttle shaft rebuild kit. Once they gain movement like that they open an air gap allowing a lean condition to occur. This can easily be mistaken as a rich bogging condition and more so if the carbs are mounted on a stock intake. The stock manifold has a cross over tract which bridges both intake ducts. It is not noticeable by the outside appearance of the manifold but it is there and has an aluminum plate between the manifold and cases...why I do not know. It seems that bolting the manifold to the cases without it should be acceptable but I'm sure Yamaha has their reasons. Anyway, this cross over will retain some fuel charge and make lean conditions of one carb or the other a bit tricky to discern. One advantage to the cross over though is that if one side goes lean you have a little bit of proper fuel charge to transfer over and help support the situation, it probably has saved more lean seize ups than most guys realize. Just remember to look for the easiest possibilities first before diving in too far, as mentioned above, it could be right there in plain sight so to speak and overlooked every time.
