I'd be tempted to fill all four boxes (frt & rear diffs, trans and transfer case) with some sort of flush fluid, drive them around just a bit and then drain them again.
Not sure if something like diesel fuel, or kerosene, or ATF would do the trick, or if there are any additives that attack other components, but once you find a benign solvent that would break down the sludge I'd do it.
You don't always want to do such high-mileage/low-maintenance flushes on the engine, but the tolerances inside the gear boxes are much looser and can tolerate gunk floating around in suspension waiting to be drained.
Then I'd refill with a high quality lubricant appropriate for each unit.
In our many discussions about what's best, I like the one-fluid-to-rule-them-all approach. Normally there are at least two, if not three different types you use on a Bronco, but I like simplicity.
The transfer case is supposed to get 50w motor oil (as oppose to gear lube), but I've used a thin, easy flowing 75w/90 fully synthetic gear lube in all boxes with good results.
Back to yours, with such high mileage and unknown internal condition, it might be best to just use the factory spec stuff and don't go all exotic with synthetics yet. You still don't know if they're going to require more work to bring them up to snuff.
Which means an 80 or 90 weight single-vis, or 75w/90 multi-vis lube in the diffs and trans, and the aforementioned 50w motor oil in the transfer case.
Sorry for the rambling. For sure glad you reduced the noise, but they've obviously done without good fluids for a good long time.
Good luck
Paul