Originally Posted by m735is

If it doesn't "settle" take it back and have him undo the work. Make sure he doesn't "loose" your old shocks.

Tough to diagnose the clunks, but even harder from the drivers seat and not even looking under the car.

Upper balljoints-just grab the arm and pull up and down on it. Any play will cause a clunk.
Sway bar mounts or endlinks.
Lower balljoints.
Could be the tie rods.
I've heard of cracked springs doing it as well.

For my CR-V it was the endlinks first, then the sway mounts, then last week or so the upper ball joint.
For my Civic it was the upper ball joint.