(Months later...)
So with all that was going on earlier in the summer (motor swap and much related and unrelated debugging) I didn't do anything with the front diff (this is my '97 Grand Cherokee) before we hit the highway. Middle of Saskatchewan: Blew the front driveshaft CV. Pulled the shaft out and continued to Ontario in 2WD. Got a new shaft at a wrecker in Niagara, bolted it in, and made the drive back to Montana. All well so far. Then suddenly, after we settled into the campground on Flathead Lake, the bad thing started.
After I hit about 80 km/hr and tried to accelerate, I'd get a really violent THUNK every few seconds - one that really jarred the vehicle. Once over 80, the harder I stepped on the gas the higher the frequency of the bad thing. Certainly felt like it was from the front end of the drivetrain, so I pulled the new driveshaft out and we came back to Calgary without further incident.
So now I think the front diff is packing it in on me. I haven't gotten underneath to inspect yet, but is this how a failing diff behaves? Has the pinion bearing finally given out and and is now causing misalignment of the pinion and a jamming of teeth? Or does it sound like something else?