hard to say what the problem is. is the bike acting like it is running out of gas? is it acting like it is flooded? or is it acting like a rev limiter?
if you arent sure which of the 3, try reving the bike in neutral to see if it will go past 10K. dont do this alot as that is pretty hard on a motor. if the bike will rev past 10K, you at least know that your ECU hasnt imposed a soft rev-limit (this doesnt mean that it still isnt the problem). Make sure that the air filter is clean and not plugged/dirty. This can cause the bike to run too rich at higher rpm/speed and flood the bike. i personally prefer oem filters to aftermarket on R6's, but that is a personal opinion. Also, ensure that the filter does not have too much tact oil on it, as that can also starve the motor for air. check your fuel filter and replace it if it shows ANY signs of being dirty. check your fuel pump to ensure that it is up to snuff. the service manual states how much fuel it should pump in a timed test. be sure it is there as the bike really eats gas at high revs. finally, what condition are your carbs in? when is the last time they were pulled apart and cleaned? if you have run bad gas through your bike or you let it sit for any significant time, your carbs can be gummed.
any and all of these items can cause your bike to stumble at higher rpm's and each needs to be checked. dont just stop at one if it seems like it is the culprit. every spring, my 99 r6 gets her carbs cleaned, new fuel filter, cleaned airfilter, fresh fuel, and fresh oil and oil change before i start her for the first time. an ounce of prevention is worth a pound of cure.
pray to god 3 times, then brake