Was curious about my bike, when I get on it while in first gear it sort of stumbles some between 9-12K rpm. I looked at the air filter and it was fine. Not sure what else to check. My bike's a 250R '02 with about 2800 miles on it.
My first thought is fuel or air starvation. That would make it hesitate only when you're really goosing it (like the 9-12K RPM range). You already checked your air filter. Did you clean and oil it before reinstalling?
Maybe fuel is the problem. If your bike sat for a while (especially if it was parked for some months) junk can build up in the fuel tank. Sometimes that can gunk up the screen before it gets into the carbs. Or it could be that the carbs are slightly obstructed from the gunk. Either way, it could have all the gas it needs unless it needs a lot. If that's it, you can fix it by thoroughly cleaning the tank, fuel lines and screens, and carbs.
Another thought is that your valves may need adjustment. If the intake valves are too tight, the engine may be starved for both air and fuel (only at high RPM's.) That would match your description. I would especially suspect this if your valves were not adjusted at 500 miles. It's a tough job to do yourself, but it's worth doing even if it's not your current problem. A burned valve (which can be caused by leaving a valve too tight too long) costs a lot more to fix than a little preventive maintenance.
There may be other possibilities, too, but those are the the first things that come to mind.
What part of Wyoming are you in? I might get out that way this summer.
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