I had a problem once with a 93 KX.... The motor revved too high once and then it went into a false neutral and that was it. I thought I had ruined the tranny, but turns out the spring loaded follower that rides around the star on the end of the shifter drum had jammed out all the way. I popped it back into place and that was it.
If your shifter fork fingers are in good shape, and the tabs on the forks are nice and square ended I would bet the problem lies outside the inner cases, which is to say that you could re assemble the inner cases and trouble shoot it from the outside...shifter arm and star/pins/follwer etc...