A little additional information in case your interested.
When you reinstall the motor the oil system will be dry, and even if you fill the oil tank a week before you start the motor the pump will still be dry ( I experienced this ). The motor will shut off if there is no oil pressure.
I was told after the fact that I should of tipped the machine on the clutch side as it would get the air out of the system as I was starting it, I don’t know for sure if it’s true but the guy who told me works for Yamaha. Research the hell out of it you don’t want to toast a motor, I got lucky.
I figured since the motor was out and that the rad hose the one on the back of the motor ( you’ll see it ) was so hard to get at, I replace it while it was all apart, I changed the thermostat as well, why not.
You may also want to get yourself a clutch alignment tool, I have checked a few and the center to center is always off, check it before and after just out of curiosity, it‘s easy to adjust.
When I reinstall the wiring I put die electrode grease on all wire connections as well.