Looks great!

1) I've never had a throttle screw try to vibrate out...  your idea sounds fine...  Some of the MX bikes came without a spring and instead has a jam nut on the screw.  That might be why?  Likely a goofy thread though but if not, I might try a jam nut. 

2) Probably normal and from storage?  Autolube check valves seep slowly and after years the bottom end of engine and even the head pipe can fill with oil from the oil tank.

3) Fiberglass muffler packing.  Readily available from motorcycle shops. 

4) Same starter and AT and CT Enduro models.  Yours looks clocked forward.  Stop might have slipped on shaft internally.  Not uncommon for the 69 to 73 125 and 175.  I'd check it ASAP...  post pics and might need to replace some parts.  A couple of members here have made really good posts on those starters and what to look for.  Yamaha made several revisions to those starters to try to make them stronger.  Most hold up great...  but many have pressed on stop slip which is common and once it starts, it gets worse.  People reset the lever on the splines but it keeps happening and eventually starter won't return.  Sounds like yours is headed down that road. 

Here it is with the cover off:

 

Closeup of kick start assembly:

 

 

Notice the wear on some of the teeth, but not all:

 

 
 

No picture, been there done that

When I pulled the kick axle out, the kick clip was just hanging loose. There is a groove on the kick gear that it appears to set in. That’s where I put it. Also, the tab at the end of the kick axle was oriented down, and the picture in the service manual shows it up. I can’t see where it would make a difference, but I am not sure.

 

 

 

Oh yeah, and thanks MarkT for the response this morning!

In regard to my question number 2, the auto lube was not hooked up when I bought it, and hasn’t had oil in it for years. I’ve been running it on premix.

That tab is the stop that slips.  I'd bet yours is damaged.  Clip is critical.  Looks like someone really kicked that starter at some point.  I'm exhausted and don't have time to explain details but check it carefully.  Really hard to tell it slipped.

If premix. then keep eye on trans oil level if stuff in pipe was oil and not fuel..  Clutch side crank seal could be bad.

Two steps forward, one step back.

While I had the right side cover off, I decided to clean and check the clutch plates and springs. They all measured in spec except for one plate and one spring. Both the plate and the spring were about 1/2 mm below tolerance. I went ahead and reassembled, reinstalled the kick axle with the stop oriented correctly and the kick clip in place.

Before we put oil in it, I asked my son to squeeze the clutch and see what it felt like. Nothing. The dang cable end had pulled off. Well, shoot! The clutch cable was adjust to the max anyway, so I clipped about 1/4” off, re-tinned the end and soldered the cable end back on. In the next post I’ll tell y’all about the step back. Here’s a few pics of the progress:

 

 

 

 

 

As you could see in the last post, I had to make another gasket for the crankcase cover. After getting the clutch cable repaired and adjusted, the clutch feels better than it ever has since I’ve owned it. That was a relief!

Filled the crankcase with 10W-30 suitable for wet clutches, and told my son that we needed to be easy on the kickstart. I told him we’re not starting a big twin! Two gentle kicks and she fired right up. We took turns riding around the yard, then I rode her out onto the county road and down the road about half a mile. The clutch felt real good. She was popping a bit at top speed, and feels a little sluggish. I am afraid I will be doing a top end soon. She’s just not as peppy as she used to be.

Now for the step back. I got back off the county road, went across the top of my pond dam, Down the dam, ripping across the field into my back yard, around a tree and back into the lower field where I turned the bike over to my son. He made a few laps, while I was sitting on the front porch with my wife. He blasted by headed to the back, then a deafening silence ensued. Now, mind you, he’s about to turn 38, so I wasn’t really worried, but after a bit of no noise at all, I figured I better check and make sure he hadn’t ran through the barbed wire fence. 

Nope, he was sitting on the bike, with a busted clutch lever and a bent up shifter.  He must have goosed it a little too much coming around the tree and low sided it. Nothing hurt on him except his pride. I had a spare clutch lever that I bought when my next to the youngest son crashed and broke one 10 or 11 years ago. So, while my son was replacing the clutch lever, I tried to straighten the shifter and it broke beyond repair. 

I reckon Tuesday I will ride a Harley to the Yamaha dealer in Tulsa to see if they have one that will work. Partzilla has one, but with shipping and all, I’d be looking at 50 bucks. 

 

 

Well, we had to order a shift lever, it finally came in and the clutch cable broke again. Bought a new one, and it is rideable again. It’s fun, but lacking some of it’s former power.

 Did a compression test, and with the engine cold I am only getting 110 psi. Repeated it several times, each time a set of 5 kicks. Shouldn’t it be closer to 135-150 psi?

I really don’t want to tear into it without knowing everything I should check first.

Well, after reading up on the compression tests as posted on this forum, and reading the article that MarkT posted from klemmvintage, I’m not going to worry about it. The bike starts first or second kick even after setting for a week or longer, and it can pull my fat ass around the yard and up the pond dam, so we are just going to enjoy it.