It would probably be a pain and not worth the $$.
The newer 5-spd auto is electonically shifted I believe, is your 4-spd? The computer would have to be changed, what else would be different in the new computer compared to the old? (not just transmission wise: 4x4 system, engine, etc...) Will the new 5-spd fit just bolt on? What other problems might you run into?
All of these are questions you'd have to think about. I don't know all of the answers, but I think the answers would = lots of $$$. You'd probably be better off sticking with the 4-spd or just trading in and getting a new Explorer that comes with the 5-spd.