Your diff is worn out. The noise could be the gears and/or the bearings. You'd have to take it apart and check everything, but rebuilding a diff is an expensive and complicated procedure. Being low on oil, or lack of service, may have damaged the diff. The seal's job is to keep oil in and dirt/water out. The seals themselves don't cause noise when they wear out.
You can probably continue to add oil when needed and live with the noise for quite a while before the diff goes out completely, but how long it will last is impossible to say.
I replaced the complete rear diff on my '01 Sport Trac last year. The OP ignored the leaking axle seals and ran it almost completely dry and then got a good amount of water in it and let the truck sit for a year. This ruined everything inside the diff. In my search for a replacement, I learned that all the Gen II ('95-'01) Explorers/Mountaineers 8.8" diffs are the same (4-dr, Sport and Sport Trac, V8 or V6). I bought a used diff w/30 day warranty from a local salvage yard for $300. It came out of a relatively low mileage '00 4-dr. It had the same gear ratio as my original diff (in my case a 4:10) and I swapped in the hole unit. It wasn't very hard to do and the replacement diff turned out to be a good one. Before installing the replacement unit I replaced the axle seals and I would have replaced the pinion seal too, but it was bone dry.
Ford says the synthetic diff fluid does not require service, but I think you need to at least replace the fluid at 100,000 mile intervals and keep an eye out for leaking seals during your engine oil change intervals. If you do that the diff can outlast the rest of the drive train.
I see used diffs on CL for around $200, but there's no warranty there if they're bad.