Hi, Tom in order to check out any main electrical system, you have to start with a fully charged battery 12.5 volts or better, and be able to pass a load test if necessary. "WARNING" never plug or unplug any electrical connector with the engine running !!!
1. Check battery terminals for damage or corrosion, check battery cables at "BOTH" ends for loose, corroded, or broken connectors, "INSIDE" and outside the cable harness, perform connector wiggle test and check cables with an ohmmeter if necessary.
2. Check the voltage drop at the battery when you hit the starter button, anything below 9 volts you might have a faulty battery.
3. Check voltage at the battery with the bike running at 3,600 RPM should be 14.3 to 14.7 volts. If you are not getting these numbers, you might have a faulty voltage regulator.
4. Make sure voltage regulator is "GROUNDED" and functioning properly, watch the video below on how to test a voltage regulator.
5. Unplug the connector to the alternator and hook your multimeter leads to the alternator (pin/socket selection does not matter) set the multimeter to AC volts, at an idle the multimeter should read 16 to 20 volts AC. at 2,000 RPM 32 to 40 AC volts, 3,000 RPM 48 to 60 AC volts. If you are not getting these numbers, you may have a faulty rotor, follow step 6
6. Set the multimeter to OHM'S, connect one lead to the alternator (any pin/socket) and the other to a ground, the multimeter should read infinity. Connect both leads to the alternator multimeter should read 0.1 to 0.2 OHM'S. If you are not getting these numbers, you have a bad stator.
7. Check all wiring in the charging circuit for worn or chaffed spots and all wiring connectors in the circuit for corroded, broken, or loose pins/sockets, which is the # 1 offender.
For more information about your issue and valuable "FREE" downloads that you will need please click on the links below. Good luck and have a nice day.
Electrical issues RPM cutting out Speedometer not working
1998 1999 Yamaha YZF R1 Service Manual R1 Moto Data Project
OEM parts for Yamaha
Btw, I’m available to help over the phone in case u need at https://www.6ya.com/expert/gregg_c0ec1df182c7330e