When you get it apart double check you're clearances, torque, and check the shift forks to make sure they aren't cracked or anything like that. And when you fill it back up us a 10w-30 SF/SG(usually labeled "for old cars"), or penzoil syncromesh. The new SJ(most common) stuff is actually a little too slippery and can cause some grinding when shifting. I don't think it has anything to do with your current issue but it may help prevent other problems.

On the bright side you will know your transmission very well when it's all said and done.