Hi, Mae3232 it should be noted that in order to "PROPERLY" diagnosis any electric starter issue it is "IMPERATIVE" that you begin with a fully charged battery 12.5 volts or better and be able to pass a proper load test, and the usual suspects are:
1. Battery terminals have loose or corroded connections.
2. Battery cables faulty due corroded or broken internal wiring at the cable connector especially the "NEGATIVE" cable which needs to be checked at "BOTH" ends.
3. Battery voltage, must be 12.5 volts or better, voltage from the battery to the main circuit breaker to the ignition switch to the security/ignition fuse to the TSM/TSSM module to the engine stop/run switch to the starter button to the starter relay to the green wire that connects to the starter solenoid can not drop more than 1/2 volt of battery voltage.
4. With a voltmeter connected to the battery, the ignition switch in the on position, the kill switch in the run position, the starter button depressed, starter engagement should not bring voltage below 8-9 volts.
If a lower voltage is produced a proper battery load test should be performed with a load tester to validate battery integrity or battery replacement.
5. Faulty starter relay, check continuity.
6. Faulty starter solenoid, check contact plate and shoes for excessive electrical erosion/etching, refurbish as necessary or invert contact plate and use the virgin backside. Check contact shoes for being loose. Replace solenoid if the negative function is still a final outcome.
7. Faulty starter, bench test starter with a 12-volt battery if negative function check, decontaminate and undercut armature commutator segments as necessary, check segments with an ohmmeter probe each one and the segment next to it for shorts. Have the armature tested with a growler and field coils, and brush plate with an ohm-meter for opens, shorts or grounds. Replace brushes if less than .438" It is generally cheaper to overhaul/refurbish a starter motor than buy a new one.
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.
Troubleshooting No Start Honda Motorcycle
1999 2002 Yamaha YZF R6 Service Manual R6 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