This is absolutely identical to what was happening to my 04 about a year ago. Drove me and the mechanic nuts trying to find it - in fact I was about to order a new computer (at enormous cost). Turned out to be a dodgy coil putting out a marginal voltage. Normally it was just enough to run the bike but occasionally it'd drop a little and the bike would die. The coils aren't cheap in anyone's language, but they're a lot cheaper than a new computer.