I had a problem on my bike that sounded something like yours. For me the problem turned out to be a slight blockage in the breather tube for the gas tank. While running, a vacume would be created in the gas tank and the bike would starve. After waiting a little while the pressure would equalize and the bike would start again like nothing was ever wrong. The way I tested it was to take the bike out on the highway with the spare key in the gas tank. As soon as the bike started to die I opened the fuel filler and the problem went away. Once the problem was isolated, it was easy enough to pop off the gas tank and clear the obstruction. Good luck.