I would strongly suspect you have a bad electrical connection somewhere. I had bike shutting down on me in the middle of a ride.
Since yours is '99, I would suspect you never took most connectors apart. The humidity/heat/occidation did their job. I would suggest going to autoparts store and getting a spray can of contact cleaner, and a tube of dialectric grease. Open up every connector on the bike, clean by spraying the cleaner, give it a min to dry, then stuff it with the grease and close it up. It will take you a couple of hours, but you will never have a bad connection problem again. That's what I did.
A couple of important points. Wear eye protection when spraying. Take your time opening the connectors so you don't break them - some of them are stubborn.