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I think it'd be a good idea to rebuild it so it will hold up to it better. I've got a 94 with a 4.0 and it's pretty tired from just me beating on it. I don't think it would hold up to a SC on it.
What transmission do you have: auto (A4LD) or manual (M5OD)? The A4LD has a reputation of barely holding up to the 4.0 in stock form. Supercharge the 4.0, and I expect an A4LD is going to create issues.
I don't know what the M5OD will hold up to, but it has a pretty good reputation.
I had a '91 Explorer with the M5OD and it was a terrible transmission. When i bought the vehicle it had 99,000 miles on it and there was a ton of play in the transmission. I put 30,000 miles on the transmission and it is still working, but not smoothly. I would recomend not swapping that transmission in if you can help it.
Well the more power you put in ,it will push your problems back,if not the trannie it will be the rear drive . I find if you put too more power up front ,you have to beef up what is behind it or it wont be able to take the torque.