The clunk you are hearing when hitting bumps is probably from the tailgate. Try lifting up on the right hand side of the tailgate at the bottom by the hinge when the tailgate is closed and you will notice their is some slack. If you lift it up and down you will probably here the clunk you are explaining when hitting bumps. I think since the tailgate has a shock absorber mounted behind the left taillight assembly to assist with the tailgate dropping it makes it lighter on the right hand side when the tailgate is closed. That is just my assumption as I have the same clunk when hitting bumps. The noise does not appear with the tailgate down or off.
Cushmanman