I had this exact same problem and searched the forum for many possible solutions. I took my concerns to a local motorcycle shop and he told me to start with the simplest thing and work my way up. I was ready to replace all kinds of stuff and he said it was probably just bad fuel and told me start there. Sure enough, syphoned out the old stuff, put some new gas in and have not had the same problem since. I was putting the high grade fuel in and he said that was a waste of money. He also made a valid point that the premium fuel is not used as often and sits in the tanks longer, giving it potential to go bad.
I agree, start with the simplest and work up...that's exactly what I did. I tried everything, change of gas, cleaning tank, filling tank different levels, re-routing the breather tube, testing it out in heat and sitting on side of road many times, had Steveo test his bike out in sweltering heat, checked controls, filtered fuel prior to filling tank, tested it in direct ambient sunlight vs. shaded light, tested it hot, tested it cold, bike would sputter and die when sitting in hot sunlight, would run ok when engine was cooled down completely..had to sit out some pgr missions cause it acted up, spent the whole summer testing.......conclusion, bad fuel pump and crap peeling from inside the pump. Changed the pump and no problems since.
BTW, I pulled my pump out with the rear tire still attached and brought it through the top rather than from side, so no paint scratching....just had to disconnect and move the wiring on the right side of the frame under the seat to have room to pull pump out.