i had an identical issue on my 95 F3. Was driving me nuts for a while as it had all the symptons of a fuel problem even though it had plenty of fuel and the carbies were fine. Would only happen after riding for a bit once the bit had warmed up.

Turned out to be the R/R. Replaced that and never had another problem. My guess is that the R/R wasn't pumping out enough power to keep the Fuel Pump going once the battery ran down a bit. Good luck.

 

I am new to motorcycle and just bought a 96 F3. Yesterday I took it out for the 1st time and cruised around the neighborhood in low speed for about an hour, and it just stalled and wont fire back up. I tried to jump it with a car battery, it worked and i let it ran as i put the seat and fairing back on the bike, not even 3 minutes later the bike went dead again... so i took the jumper cable out and tried to start it again, this time it stalls as soon as the rev drops below 4000...

is this an alternator problem? there's plenty of fuel in the tank, and the battery was replaced 3 years ago. Finally i borrowed a friend's battery off his R6 and rode it home in 1 piece... any thoughts?