No need to swap both axles, just make sure the gearing is the same in your donor axle.
The Explorer axle will be spring under, so you'll have to move spring perches and shock mounts. RuffStuff Specialties can help with that:
http://www.ruffstuffspecialties.com/...g/88SS-31.html
As far as I know, the width is the same in your 2000 to the Explorer.
'91-94 Explorer axles will be drum and should hook up directly to your current brake system. '95-2001 is disc, so you'll have a little to deal with in hooking up the parking brake.
Lots of write ups on this swap at various forms. I think there's a good one in the TRS technical section.