Is the "clunk" sound coming from the rear? If so, and if you don't already have it, then buy the AXR clunk fix. Should fix that problem pretty easily.
As for your 2nd concern, does it only happen when you hit bumps?
I had a bad clunk in the rear. When I looked under my car I noticed that my endlink mount on the strut had broke. My endlink was resting on the sway bar.
In which case I recommend you check all of your endlinks to see if any are broken.
Then I (and everyone else who has it) highly recommend buying evolv's clunk fix bracket!