just wondering if you ever figured out this problem because my 04 1000 is doing the exact same thing...........about 9grand the bike will will stumble around and sometimes at 6 grand if i am on the trottle 3/4 to full the bike will not go past 6 grand, sounds like are problems are close to the same, i have had no luck checked fuel lines, airbox, ran lucas gas treatment to clean injectors, im kinda at a loss....

 

i forgot to tell you that i have removed the exhast servo motor flap, i checked and the servo was not operating right leaving the door shut on the exhast and building to much back pressure when at open throttle, it made the bike do this wierd lundging motion, it would lunge forwad then the power would fail and repeat all the way down the road, so i removed the cable to the servo and removed the flap, which made it basicly a higher flow than stock pipe, feels snappier in the throttle response but didnt fix this remaing issue

 

No haven't found the problem yet. I've got a slip on yoshi that removes the flapper in the exhaust, I did leave it connected however so I didn't throw a se light.

 

after pretty much checking everything, i think i found the problem... make sure that all of your fuel lines and drain hoses are in there holding brackets under the tank, and there is a set of wires that run under the tank as well, the wires were getting caught under the fuel line as the tank slides back into place, once i made sure that the wires were clear and set the tank down carefully havent had the problem again and rode it 4 times all 100 mile trips, i know this sounds to simple but hey worth a shot it fixed mine, mabe the wires were keeping the fuel line from expanding all the way under high demand, try and see if it works for you, good luck