KDX engine cover HELP!

For some reason the right side engine cover is allowing me to install it but it is not fitting flush in the corner where the shifting shaft is. I have tired about 100 times everything fits together fine(dowels etc.) but I get a small gap on the bottom(1/16"). No gasket seal(I can move the gasket around). Tried tapping with a hammer. Tightening with the bolts. Removing the shifter shaft to see if it was stuck out to far. Nothing.
Has anyone had the same trouble? Am I not holding my mouth right????
It is a very simple install that is kicking me in the #%#.
Thanks. Neil.

As an update. I solved the problem.
The shifting shaft has 2 forks on it. One moves independent of the other. Somehow the one fork moved, popping a detente collar out. This will make the shaft sit proud by an 1/8". Making it impossible to reinstall the cover.
Hope this may help someone in the future.

Neil

Thanks.
Finally a buddy asked if I had removed the shifter shaft and then tried to install the cover. There was a long pause and a lot of swearing......
2 heads ARE better than one sometimes. I was so frustrated I didn't think of the obvious and simple.
It worked, so I had to figure out why. I was very glad to be able to install it very easily after that.
Then it was on to the cylinder which I got back from the machine shop. Nice and clean with a bag of dirty parts. I didn't tear the cylinder down, the machine shop did. What fun it is to put something together to didn't, take apart.
Anyway. the bike is almost back together.
Need to get cutting trail for our next race. Zofka Ridge in Hope BC Canada. Bike has been down since our last race in March, The Bent Spoke on Herrling Island.
To long no bike....

Neil