take your carbs apart and thouroughly clean them, make sure all jets, needles, passages are clean. if that dosent fix the problem you may need to rejet your carbs, did you move reciently to a higher or lower elevation?, did you install reeds, boost bottle, pipe, intake mods? this could be the reason why it runs like crap at higher speeds. pull your spark plugs after a lengthy ride, what color are they? (white) means lean, (brownish) means you are in the ballpark
if all of this does not help try this!
if you have mikuni tm 38 flatside carbs try turning the mixture screw (located on the right side of the carburetor towards the bottom just above the float bowl) counter clockwise 1/4 turn on each carburetor (this will richen the mixture) possibly solving your troubles.
also what is the condition of your belt? it may be worn which is causing the clutch to shift improperly, this intern may be killing your top end!
if your track is too tight it will bind resulting in poor top end performance
check your chaincase too, make sure it has oil in it, and that the chain is properly tensioned
BRAAAAAAP!!!