When I get a new / old motor, I'll tilt it up, remove plug, rotate piston to near TDC, squirt Deep Creep into cyl. and let sit, then repeat a few times to each cyl. over the course of a day or two. As you rotate crank/pistons the deep creep will run down exhaust and loosen gunk and carbon in exhaust system. Do it in early spring so you can start motor while carbon is still soft.
You'll get huge clouds of white smoke and sludge dripping out of exhaust .. warn neighbors ! … LOL
It could (Maybe) even out your compression numbers (Maybe) ..
I also (on new/old motor) replace all fuel lines, fuel filters and oil lines. Also make sure your fuel tank is clean and rust free if it's metal.
Not sure if this applies to Yamaha's ..
But I check oil pump linkage to make sure it set to open fully at WOT setting.
I pump a shot or two into grease zerk on motor, I get a few drops of water out of steering swivel every year.
I'll add Star Tron to fuel tank, run motor till treated fuel is running into motor, pull fuel line off motor, run as long as it can, then remove float bowl drain screws on carbs to drain the last small amount of fuel left in bowel.