I would start here. This is a posting (2) that was put up by another member,(Arfstrom thank you!) that helped me greatly. Here it is:
So, I had already pulled off the cap with my finger tips. Underneath I found the Lock-nut, and screw bolt for adjusting the Clutch.
I used a 12mm Deep-well socket to set the nut, while I held the screw in position with the screwdriver.
Then I put the plug back. I suspect the 2 screws is for the older systems.
When I got to the top clutch handle, I found that the inside clutch cable had a lining, and it was being pulled out by a ratcheting effect of the normal clutching activities. so that means, if the pic turned out any good, the gray matter stuck in the handle zone, is extra I started cutting it out, then re-built it again, only to find out that no matter what I did, the gray covering was going to be pulled out. So I continued to remove it.
Now that its put back together, I can feel the spring effect, It seems to be a totally different feel for clutching. Now I wonder if the overheat symptoms where more to do with the clutch handle being fouled, or not. Perhaps Tomorrow I will find somewhere to get her to overheat.
You can see the gray thing being fouled up, and then next shot was the longest length of it that I cut out.
I followed the manual explicitly, I had printed out the segment I had copied into this posting earlier, and read/re-read it, till I knew I did right. (what I am trying to say, Use the manual, as well as google)
I would also make sure that the shift shaft has not been pushed into the case, there is a circlip holding it, if that happens it will push the linkage apart on the clutch side. Not a tough fix but a pain in the butt.
I did this adjustment and it worked perfectly and solved a very similar problem that I had after having the clutch adjustment side cover off. Good luck. Here is the link to manuals that you can download....
http://www.xs400.com/threads/yamaha-xs400-manuals.4503/ . You are going to have to start with these I think.