Hey!
My daughter's 93 4runner (4x4, 6cyl, 5 speed) had much the same problem as you are describing! Being relatively new to the Toyota's we returned it to our friend's garage.
The mechanic stated right away that the Clutch had air in the lines and needed to be flushed out! After this procedure, the truck shifts like new!!!
I can't say that this specificly is your problem, but It sure sounds like something I would have looked at!
Hope this helps in some way.