When I was removing the rear wheel to replace the brake shoes, and also ended up replacing the rear wheel bearings a well, I only took care was on placing all the parts as I removed them in a place where they would be safe for later cleaning and reinstall. After getting the bearings in with the new seal, brake pads on, I set the wheel in place and slid the axle in. Once it was in place and ready for the nut to go on to tighten it all down, well I noticed a gap in the assembly that I never thought would be there. It was about a 1/4" gap where it seemed like the swing arm is wider than all the parts that make the rear wheel function as it should. On seeing that I went back to the parts illustration to make sure I wasn't missing anything, just to be sure. All parts accounted for. I did that twice on different occasions, since I was hesitant to tighten everything up just yet. Using 2 different illustrations to confirm how it went together. The Clymer manual I got for the bike and the parts illustration at Partzilla.

Everything was in place as the pictures shown, so I tightened up the axle after the chain was adjusted etc. When it all drew together the hole drilled in the end for the cotter pin was beyond the castellations on the axle nut. Like the space I noticed in the line up should have a spacer in it so the cotter pin if applied will set in the notches of the castellations like it's supposed to.

Maybe I am being concerned over nothing. The rear wheel spins free, it is all tight, and if I used a cotter pin, the axle could loosen up a bit but  would not loose the nut....

I am looking for any info you guy might know about my observations, if they should be a concern or not.

Thanks in advance.

This site has been a real help in my adventure in getting this old bike going.

Uh-oh.  Sounds like a spacer or spacers might be wrong length? 

Unusual for nut to tighten down to where pin doesn't go through castle nut notches...  red flag for me there. 

Maybe post some photos of the set up?

 Shows two bearings on the sprocket side. Hate to ask sorry,--not accidentally left one out. Long spacer in the center as it should be, Can't think of any other things easily missed. If it's gone past the castellation part of the nut & split-pin area then it's likely about run out of thread on the axle.

3 number 9's
www.partzilla.com/catalog/yamaha/motorcy...973/mx250/rear-wheel

All 3 bearings are in there and the spacer between them. I noticed that when the seal went in it did recess into the bearing bore more than I thought it should, but the wear marks on part #28 agreed with the depth it was set. This is one place I really wished I had taken notice of the orientation of the parts. I will get a few pics of the situation.

Does the brake plate rub at all on the wheel hub? On my DT1 I once had a spacer that was supposed to be on the inside of the hub between the hub and the brake plate, placed on the outside of the hub. I was hearing a scraping sound and saw some aluminum filings collecting sound the lip of the brake plate. I had also noticed a gap like yours. Switched it around and fixed the issue immediately. I think part 11 on the schematic you posted. 

In response to  Adguy, The wheel appears to spin freely that I can tell for now, the chain is on, the bike is in gear without the cylinder on. I just got the upper bearing to put it on just today!! I am rather tickled.) But for the little I can turn it, I hear no sounds that are out of the ordinary. Also I got to give credit where credit is due... RT325 posted the diagram, I haven't figured out how to do that yet.

Now onto the pics of the situation. The first 2 pics are with the axle tightened up as I left it a few days ago showing the threaded end and the nut, Others are there to show all the components in the line up and one of the pics show the gap while everything is loose.

  

These are pics of the loose arrangement.

 

The only thing that is not like the diagrams are the direction I set the axle in, but that should not matter in this.
Thanks again guys...

Thanks for the pics, but i'm out of ideas sorry.

I had a thought, is there anyway that one of the members may have 2 framing squares handy that could be used as a large caliper to measure the outside faces of the flats where the chain adjusters go? The framing squares should be large enough to go around the rear wheel without removing it. That way I could see if my swing arm is spread, or perhaps I could simply add 2- 3/4" flat SAE washers to fill the gap. I am not crazy about the idea, but if the dimensions say it is the correct dimension before I tighten everything up, cuz the axle surely could spare it, and if the wheel acts as it should, then I do not know what else could be done... All the proper parts are there that I know of.