I started to ride to work on Friday ( twenty miles one way) got about four miles from home and it abruptly started to run on one cylinder. Turned to limp it back home and made it about a mile when suddenly it popped and started running like normal again. Still took it home not wanting to get stranded. Haven't had a chance to pull the tank off and have a good look around yet but it sounds an awful lot like how other members have described their CDI going out. Crap just got it back from the dealer a couple of weeks ago for the 12,000 mile service too. All it takes is money and desire I guess. Maybe the dealers mechanic left a wire loose ( I hope)
If it happens again, note which side is still firing. Swap the wires (primary and secondary) between the 2 coils and see if the problem switches sides. If it does, you probably have a coil or wire failing. If it doesn't, then CDI is toast.