Dude I Own an `03 F4i, and I'm Having the Exact same symptoms, I just did a Full "Tune-Up"( I'm at 12,300) and I'm now running Full synthetic, I also changed the Oil Filter, ReCharged my K & N, and put in 4 NGKs(spark plugs, they ain't cheap!$83 OTD from Honda dealer!) and I Tested it after, to see if tghe same problems exist, My Bike STILL, After running Normally for about 20 mins, F1 light comes on, bike runs herky-jerky Rough, almost quits!! I've Heard that there is a particular part that even Most Honda Techs won't tell you about, or don't know too much, it's the "Fuel Pressure Return Regulator", it's like a Diaphram, On the throttle bodies, it Can and Does tear/Break/malfunction, and I've heard that IT needs replacing, If the fuel filter etc are still good( I've been narrowing it down part by part myself trying to figure it out!!) Then call your local dealer/Parts( Try Online too) for that part!! My bike seems to Be running quite HOT( above the Normal temps, by around 40-50 degrees) so I'm going to replace my thermostat as well, and see if it STILL cuts out, or Almost does!! Any other questions feel Free to hit me back & Good Luck!!!!