Well, I've isolated the 'clunk' noise to the latch on the rear hatch. (as suspected!)
I put a small square piece of cloth on top of the tailgate over the latch recepticle for the hatch (so that when the hatch closed, the cloth wrapped around the latch and slipped into the latch opening, cushioning all of the internal workings) The cloth was thin enough so that the hatch still latched securely.
When I hit the offending bump (that causes the clunk EVERY time) this morning... nothing. So it definitely must be some part of the latch assembly that clunks over certain types of bumps.
Now I just have to figure out if there are any particular bits that I can muffle with felt tape to keep things quiet
