Air,
My bike ('02 BA) is acting much the same way and I too am baffled. It has run flawlessly for over 7k miles and now 3 weeks before a planned 2 week tour of the west coast she starts acting up -uuuurrrrrrgh!
My bike starts fine runs okay for a few minutes then begins to miss. A few minutes later it looses power and stalls or wants to stall. I don't beleive mine is fuel related as it seems to run better with the throttle wacked open and at higher revs. I would think if it were a fuel problem it would get worse. I thought I might have screwed something up when I installed the tach a few weeks back so I removed it but that didn't change anything plus it ran for a few hundred miles with the tach with no problem.
I'm starting to think it must be a coil or some other electrical gremmlin. If you figure it out please let me know.
Thanks,
Keith