Hi, Tom if your headlight is not working, keeps burning out, blinking, or is dim the first thing you need to check is the headlight bulb for damaged filaments then check your light circuit fuse, then check your head light bulb socket ground wire for a clean tight connection, that being said the usual suspects are:
1. Faulty ground or power supply wire to headlight bulb socket.
2. Worn down solder contacts or loose fit of the bulb base in the socket due to vibration.
3. Worn, chaffed, or broken wires in the light circuit.
4. Corroded, broken, or loose pins/sockets in wire connectors.
5. Faulty hi/lo beam switch.
6. Faulty ignition switch.
7. Fuse is good but no continuity on both sides.
8. Faulty wiring between battery positive and headlight bulb socket.
9. Weak charging alternator/generator.
10. Faulty voltage regulator/rectifier ground or overcharging.
For more information about your issue and valuable "FREE" downloads that you will need please click on the links below. Good luck and have nice a day.
R1 1999 speedo problem
1998 1999 Yamaha YZF R1 Service Manual R1 Moto Data Project
OEM parts for Yamaha