This may or may not be relevant to your situation, but here's what happened to me: about 9 thousand miles or so ago (have 12,850 now) I noticed sometimes I had rough running, and inconsistent smoothness at idle. Seeming to misfire sometimes, inconsistently, revving it from idle in neutral would sometimes produce a misfire/backfire. And a general down on power feeling. Sometimes I'd go to WOT and swear I was missing 20 whp. After a bit the big DUH factor kicked in. When I was putting gas in her, I would ride up to the pump, and I was mostly using an off brand, and fill er up with the highest octane, 92 in my area. Anyway, all these pumps I was using have only 1 (one) hose that comes out of the big housing, splitting off from the 3 grades down in the housing. So whatever gas was last pumped would be the first gallon or gallon plus that flowed into my bike. Each time any customer got gas, the fuel shutoff leaves the grade of last used fuel from the internal splitter to the nozzle. So every time I was gassing up I was randomly and most probably usually getting the first gallon of shite 87 octane Kawi killer gas. And I liked to get gas alot when down to a half tank so when ever I started I'd be full. I started religiously fueling only at chevron or 76 and only at older stations that had the individual pump nozzle per grade. Presto, problem went away. Now problem is morphed into trying to find a pump when I pull in where the last sale was 92 octane. What's happened is that all the older stations near me have retro fitted their pumps to the one nozzle style so I can no longer just confidently pull up and use the individual 92 pump. Now I have to make a big production of finding a pump that last pumped 92.
I've even had to once finally offer to give a random stranger a free gallon of gas cause I couldn't get a last used 92. That was frustrating but the fellow was understanding an happily took the first gallon then moved to the next pump. So in my case the fuel situation is crucial. I do have the 2WDW reflash, and not even the stock one at that, mine was tuned on the dyno, so I may be more sensitive than most. Anyway, sorry fer the long windedness, but my problem did go away. Moral of the story: very fuel sensitive machine.