1) Inspect the drive line very carefully, U-joints normally give visual signs before they fail.
Look carefully for any splitting of splitting, or cracked edges of the U-joints. Also look at the intermediate bearing (between front and rear bearing.) The photo is a U-joint on my Ole Toyota MH, the Ford will be larger, but this gives you an idea of what you might see if its failing.
2) Tailshaft and park brake assembly.
The park brake internal bearing can fail and start causing a lot of play on the drive shaft splines, i.e. you can move the drive shaft up and down where it goes into the back of the park brake.
If this bearing gets to bad, it will destroy the tailshaft of the transmission. very bad news.
Park brake assemblies are re-build-able. Usually they fail from lack of oil (they require servicing) but the tranny tailshaft is a big ticket item. Catch it before it destroys the tailshaft.
3) Engine misfire could cause a momentary hesitation that could cause the clunk. You need to read the "Check Engine Code" codes and post them so we can better address your question.
2001 Coachmen Mirada (Ford F53 6.8L V10) - Toad 2003 Saturn Vue.
It won't do MACH 2, but I can get a sandwich and take a pee.