Check your electrical connections. Battery cables (at both ends), fuses, backside of the fuse box, igniter, etc. Especially those under the tank. My theory is that, as things warm up and expand, you loose power to the ignition system. When the bike stops, heat rises from the engine and expands stuff even more and it makes contact again.
If it ere fuel flow, you would ride along fine, sputter to a stop and sit for a while whilst the system fills up again and then repeat all over.
