If the starter is engaging with the gear it could be the sprag clutch has failed/failing. This sits in the back of the rotor housing/generator and is a one way clutch. What happens is when starter engages with the gear the rollers in the clutch engage onto the crank and spin the engine, the engine fires and the rollers dissengage. Over time the rollers delelop flats so they dont roll very well and grip the crank and the springs behind them weaken. On big triples and twins this can be a problem as batteries get weaker and havnt got the whack to turn the engine over fast enough which in turn puts strain on the sprag clutch causing it to fail and in some cases cracking rotor case/gear. But I doubt it if it will be that bad on your bike. This is what the sprag clutch looks like as an example. Genuine Yamaha Sprag clutch 21CE558010 & Gasket YZF-R125, WR125, MT125. | eBay