Check the charging system. Older Yamahas are notorious for regulator/rectifier problems. Voltage across battery terminals with the engine running should ideally be 14.something, those older regulator/rectifiers might be low to mid 13's which is still tolerable for a flooded lead-acid battery (conventional), but it should at least be higher than the voltage across the battery terminals with the key switched off.
On the FZR regulators, there is a little ground connection that is meant to be attached to one of the bolts for the regulator ... if yours is like that, make sure it's there and properly connected.