I've had the carbs out quite a few times trying to get them running right.  The first time I could see that the main jets were plugged with black goo.  Gave them to the mechanic friend to clean, and at least it ran.  It even seemed to get better with a few miles.  Then bike sat at his house for a couple of weeks while he got around to doing the fork seals.  And it wouldn't run again.  It would idle, so the pilot jets are ok.  I've since pulled the carbs, cleaned them again myself, and drained and replaced the fuel, but it just does run perfectly.  There's a real noticeable stumble between 3,000 to 5,000 RPMS.  Then it takes off like the afterburners came on.  Could it be that the Needle Jets and the Jet Needles need some attention?  I'm running stock exhaust and air box.  I also noticed that one of the O-
Rings on the end of the float bowl assembly is chaffed.  What is the purpose of this O-Ring?  Could this be causing the stumble?  Thanks for your help.

Howdy Mr Buzzin.
I had my carbs apart cleaning and rejetting and it did the same thing. Very flat spot in the acceleration but I could throttle past it and it would actually jerk bad and take off after that.
I had not removed the emulsion tubes. When I finally did, one tube had a black build up on it that had all 4 side holes plugged.
Take the carbs back off. Remove the bowls, floats, carb top plastic covers and slides. Unscrew the main jet 1 or 2 turns and tap it like you're trying to drive it back into the hole you just unscrewed it from. Use a plastic screwdriver handle or something soft but you'll have to smack it pretty hard. The Jet will be forced down forcing the plastic housing out of the top of the carb that the slides slip into. Repeat; unscrew a turn or 2 and tap again forcing it out more. After a couple of time at this you'll have the plastic out the top and the emulsion tubes will be exposed. There is a O ring there also that I found was mush.  After replacing my O rings there and cleaning the tubes "small holes in the side of the shaft" mine ran great. No more flat spot.    
I saw a distinct trail where gas had gotten past that o ring.
This may not be your problem but it was with mine. Mine is a 96 that only had 1694 miles on it at the time. 1500 mile later it purrs..
My flat spot was really noticeable more in 5th & 6th gear. 1/4 to 3/4 throttle was dead then BAM!!!
PS. My opinion... The o ring on the back side of the float is a mounting means for holding the float assy up in place and if bad will also allow fuel above it to leak back into bowl and or float to drop out completely if not tight. The O ring on the float needle seat holds the seat in place and when bad will allow fuel in the inlet line to the carb to drainslowly to a level above the float. Such a case could eventually drain the tank.