Fuel pump maybe???
 

Still can't figure this out!!! 01 f4i.. Pretty much stock, just two up rear sprocket, 19,xxx miles. One day I'll ride and have no issues and the next time I ride it'll act up. I have, with my limited mechanic skills went completely over my bike and everything seemed to check out. But the time I ride and have issues, here are the symptoms. I can ride and my bike will act like it starves for fuel/fire while riding...and while I notice this while riding it quickly gets back to running. Like a sputter. When it doesn't get back to running I'm on side of the road, all electrical works, I get everything but the sweet noise of the fuel pump prime. Then after a few phone calls for one of my buds to come rescue me, when they arrive, I'll will try attempt to start it and the fuel pump primes and the bike is good to go!! This is an occasional. Would the fuel just work sometimes and then not? I figure if it was, wouldn't the pump go out and stay out (burned up)? I recently before this stuff started, I did a routine tune-up.. Plugs, oil, air filter(k&n), sprockets, chain, took the triple off to tighten my stem bearing, was a tad loose. In order to take that off I had to loosen and move to the side my ignition switch. Could that be the culprit? Bout to give up and take a torch to this thing. Help would be greatly appreciated!! Be safe!!!!

Could be a kill switch issue. Have you checked that? See if flipping it a bunch of times when it's acting up brings the pump to life.

Yeah, that's one of the first things I do. The last time I rode, u just left in the on position, never used it to kill it like I normally do. I would just use the key or the kickstand. Didn't seem to change anything. Is it possible that the fuel pump is getting hot and shutting down? Then when it cools it'll work? This crap is driving my crazy!!! Lol!!

Replaced the ignition switch,bike wont start HELP
 

Had the same problem as the OP, opened the ignition switch and sure enough one of the wires had disconnected. I soldered back in and the bike ran fine for around 1000 miles (bike has almost 40k) then it started acting up again. Soldered once more and ordered the oem switch from honda.
Installed it last night, bike started fine after install (before tightening up everything) then once again after tightening all the screws and it started and ran just fine. This morning i go to start it to go to work, i turn the ignition, the pump primes all the lights turn on but the damn thing wont fire. Checked Fuel 1/4 tank, checked all connections & reconnected all, charged the battery (died while trying to start it), visually inspected everything, NO DICE. The bike always ran great, never any hezitation or sputtering and fires up within one sec of hitting the starter. HELP !!!! PLEASE !!!! This is my ride to work, and everywhere else. I don't own a car and need it running.