I'm thinking your throttle cable is on upside down, if I'm not mistaken that hole in the top is for drainage.

Or is the hole for access to lubricate? I've seen many pictures with it in this direction, and it's hard for me to believe the original owner I bought the bike from had the throttle off. I've also seen the throttle in the other direction with the hole on the bottom.

In my opinion and experience hole goes on the bottom on every one I've had... And all Factory Yamaha manual, parts lists, and brochure photos all show it that way?

Alright, I flipped the throttle so the hole is at the bottom. I really just wanted an excuse to do so as with the hole up the metal portion of the cable housing was interfering with where I wanted to position the front brake lever. Again, I gotta' figure this was how the original owner got the bike, but no big deal...

As for the foam under the tank, mine had to have been 50 years old. If/when touched it'd crumble and make a mess everywhere. The upholstery shop that attached my new seat foam and cover provided me with another piece to use.

 

It's possible it was assembled wrong originally. 

A few years ago I bought a bike (not Yamaha) from the original owner who rode it one time back in 1977.  Front brake cable looped way up in the air above the handlebars.  Lower fork sliders on the bike both had a slot for the brake plate and it was assembled with brake on right side instead of left side.  I turned wheel around and all was good. 

Of course the owner could have done this but he said it was never touched...  Both tires were original with only very slight wear to the rear tire.  While I had the wheel off I pulled the tube and it was original with no patches so I'm pretty sure dealer put wheel on backwards.  Research showed that in earlier years this model had a shorter brake cable and did have the brake on the right side.  So that made the mistake even more understandable. 

Sure did look "wrong" with that big loop of cable sticking up so you'd think someone would have questioned it but they didn't. 

Looking for photos of cables/wiring under the fuel tank.  

Thanks for all the photos.  Really helps to get mine back together after restoring.
 

I don't have any good pics of the cable routing under the seat. I've not had to mess with the wiring yet.
 

 

 

The black piece of tape seen in the first pic I put there to hold the wiring up to the frame, it wasn't originally there. The black wire coming across the rear fender from the right rear turn signal may not be correct. The turn signals on the bike when I got it weren't correct. I've seen the wire cross over a bit more forward under the piece of frame cross over. It could have been done, but would have been tight to do so, so I crossed it over where I did.