Usually this problem comes from bent shift forks. I would probably just put a new transmission in, it would save you a fair amount of down time. If you REALLY want to tear into your transmission, you can check out the FSM
www.nicoclub.com/FSM and see what is involved with changing out the shift forks. You'll also want to check the coupling rings and where they interface with the gears themselves to make sure that everything is in good shape.
In all honesty, it will probably be cheaper and easier to just pick up another transmission. If you have any questions about what you need to do, we are here to help you.