That's just an aging transmission. Mine does the same thing, its an Si 5-spd (L3) with around 50,000 miles on it that I bought from a shop. It doesn't grind, but like you say, sometimes it just refuses to shift into a certain gear. Other times it's smooth as butter. Try putting some Lucas Oil in the tranny. Mix about 30% Lucas in with normal tranny oil. That will help. Otherwise, don't abuse the tranny until you can afford to rebuild or replace it.