30% of the way there...

Polish the chrome and move on.
If you’re going to ride this bike it will get covered in dirt and you can’t see it anyway.

 

To prevent possible rust through , you could clean off most rust, then de-rust with something like Evapo-Rust, paint if desired, then spray with undercoating.

 

Another vote for rust treatment and undercoat spray.

Excellent work. Can’t imagine how many hours you must’ve put into this project.

 

That fender is perfectly normal.
I think any paint you put there will flake anyway. If you’re worried about the rust just rub oil into it. After riding I’ll bet it looks like this again anyway

 

I think I'm going to wire wheel the rust down to the base metal, prime and paint.

While I ponder, I'll begin on the engine.

 

Whew!

 

I know what I'm doing... (nervously shifts eyes left and right)

 

3 essential tools for any build...caffeine, nicotine and blue shop towels.

 

Did you change the chain guide? Not expensive part and it will save you a lot of work in future when the old one breaks up . Heat the bolts to soften the factory loctite and fit new bolts and torque then to spec.

 

The OEM one is in fantastic shape.

 

Small victories.

 

No one likes crusty nuts.

 

My concern is that I'm going to be using Permatex Ultra Grey and not Yamabond 4... I hope it's a suitable equivalent.

 

She's coming together.

 

F#CK!

Because neither of shop manuals that I have were clear on it, I now have tear apart the engine that I just spent all day putting together, because I have a shim on the middle gear in the wrong place...

 

GRRRRRRR!

 

I'm now at a standstill on the engine.

I'll start polishing the chrome tomorrow I guess.

 

Sorry to see that. At least clutch baskets are still fairly easy to get on eBay, etc.

 

While I wait for replacement parts...