May not help but I would put a bottle of Seafoam or my favorite, Gumout for high mileage engines with PEA, in a tank of gas and run it through. I suspect (just wild guessing here) though that your bike may be experiencing weak spark after it gets hot. Could you test the spark when it starts running rough? It's hard to check on all of the exhaust pipes on a Gen 2, but if you could check the exhaust pipes temperatures, it may tell you what cylinders are not firing. I have one of those infrared thermometers and it is a big help with this. I think they are as cheap as about $20 on line or at harbor freight. I paid a bit more for mine at Autozone.