Some 90s explorers come with 8.8 LSD and 3.73 gears. I know they are 31 spline so maybe you can use your original axles and just swap in the center guts. However if you have 4x4 then you will need to do the same in the front. You always want to match gear ratio front and back unless you are just upgrading your differential from open to LSD or vice versa

 

My '07 5-speed also has the 3.31 rear. From what I was able to find out about the 3.31 gear it seemed to be telling me that they decided to use the existing F-250 chassis because it came with the 3.31, so they were able to advertise the 4.2L XL with 5-speed and 3.31 rear as having a higher load rating. When you check on the 3.31 it indicates F-250 which seems to confirm this idea. I believe the idea was to help the 4.2L get better highway mileage, and the gear set in the trans is designed for this rear. If you put in a 3.55 or higher, 1st gear would then become a 'granny' and be useless in traffic. As it is, its still low with the 3.31 but is adequate for a reasonably fast start in traffic. And, it moves the truck very well with a load.
With an automatic trans a lower gear doesn't cause as much drivability trouble and provides faster acceleration.
Just wondering, in the digital age, how do you correct the speedometer when you change the final drive gear? The ECU depends on this info for a lot of functions.
I think the first thing you would do with a 4.2L truck is find out how to get rid of the throttle opening delay that is built in for some reason. For example, I can 'blip' the throttle with the clutch in with a quick release and the engine won't do anything. During shifting, the engine always bogs after the shift, but if I hold the throttle at about half throttle, it gradually opens the throttle plate over about 5 seconds and it accelerates well. It would be great if that delay wasn't there. I just like a mechanical throttle, being sort of 'old school'. Back in the day, if the engine bogged on throttle, you knew what to do to the carb and timing to get the response you needed. With this thing, its a matter of reprogramming or deprogramming.