I had the same problem on my 500. Stock air box with stock filter, put a 4 in to 1 exhaust on because the old one was rusted out. Found that the bike had a flat spot at 5000rpm when accelerating at 1/4 or so throttle. Lifted the needles a few positions to see the result. Flat spot gone, but had the same "blubbering" or rich running condition at idle to 1/4 throttle. Had to blip the throttle a few times to clear the engine before I could take off. Used a color tune plug to see if I could clear it up with the air screws, no luck, too rich. So I dropped the needles one spot, repeat, and repeat. Runs great now.
Just take your time, change ONE thing at a time to see the result, write it down if you have to. People seem to panic and change ten things at once and then can't figure out what did what. Just my two cents.