Not meant as a jab or insult, but ... Are you sure you weren't lugging it a bit? If not, I would try a good fuel system cleaner ... I've personally used Ring-Free by yes, Yamaha with great results in the past for removing carbon deposits. Should change your oil after running a tank of fuel with it.
Another good trick that won't cost you a dime for knocking off light carbon deposits is plain old water in a spray bottle that puts out a fine mist. Just yank your air filter and raise the throttle just off idle to keep from stumbling and spray some through. Pull your plugs before and after for comparison. If neither of these help, then you better see someone that knows how to tune it properly .... that seems to be few & far between these days. Never go to a dealer for a tune either ... MOST of them are flunkies that just load generic canned-tunes into your ecm and don't take the time or have the know-how like a reputable tuner does everyday for a living.
BTW ... raid the old lady's bathroom for an empty pump-spray bottle from hair spray or something ... they put out a real fine mist if you choose to try the water. I keep one in my saddlebag with water for those pesky bugs out on the road.