Well, guess I'm not sure how Ford approaches that job. I assumed a tranny
pull, which means the transfer case comes out. Did they pull the engine and
tranny as a package instead?

I have the 99 AWD. I would be surprised if a clunk had anything to do with
the differential itself. And just for the record, my front seal leaks. I
check the fluid occasionally, but even tho the differential is "wet", it is
not losing enough to require adding fluid.

It can be tricky finding drivetrain noises on these things.....