Mate I just bought a 94 RM with gearbox problems similar to yours, only it had lost a bunch of gears. I pulled the box apart and the shifter forks were stuffed, they have small lobes on the ends of the fingers on the fork, and these wear off in time (im my case cos the previous owner didnt put any oil in it). I am willing to bet your prob is the same one, shifter forks. I reckon you would be best replacing them all, as youll be splitting the case anyway. For my RM they cost $35 US each from bikebandit. Your bike will shift like a new one when you do the job!
Happy to talk through it in detail for you if need be...its not a hard job.