Caveat on pulling the shift shaft out - if you've bent the shaft, and its not uncommon - it may get stuck on the cases on the way out. In that case if it does come out its not going back in.
Here's what my problem was, just as I suspected. My right side case was a real struggle to get off too.
Gave me a chance to check my impeller and adjust the slack on my power valve also.
I haven't put anything back together yet, still waiting on 2 water pump cover gaskets, power valve cover gasket and a new shift shaft. I'll have a look at the surfaces.
The fork parts are stamped, and sometimes not smooth and true. Look carefully you will see. Work the edges with a fine file and then a stone, test fit the parts, it will be obvious.
