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I agree with at least checking the clutch adjustment. These engines are notorious for having a little clutch fade as they get hot. I often readjust my clutch a little once the bike gets hot because of it. If your clutch is already adjusted on the loose side when cold, it will almost certainly be etremely loose once warm and you can have difficulties with down shifts and neutral.
How old is the oil and what is the level reading at? If you haven't changed it recently, I say do an oil change and see if you have any larger shavings or chunks of metal in the oil or filter screen.
I also agree with checking the chain, not just for tension, but for front to rear alignment. Sometimes you can get some odd noises from sprocket misalignment, and in this case the countershaft sprocket being in an overdrive gear might be causing some strange vibration resulting in the noise.
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