You have to remove the trunk liner and cut through the black rubberized-paper grommet to fully see the condition of the shock mounts. If they're loose or defective, you'll notice.
What springs did your rears get replaced with? If they're not OEM, you can easily have a low-speed clanking noise because they'll bind. The spring pads could be installed incorrectly, off center, or otherwise causing this issue as well.
I somewhat doubt it was the tools though. The battery compartment is also an area where you could have something rattling around.