To answer the questions:
My dad's shop did the work, and yes the subframe was removed from the car. The subframe brackets were welded and reinforced. I think the ABS sensors or something were replaced as well (apparently they broke when he took them off). Rear rotors and pads were changed, as well as shocks and struts.
You've got me thinking about the backwards sway bar...that could be the problem. Isnt' there a kink in the bar on towards the one side (i though it was the right side). If so, I could see how switching it would make a difference and cause a clunk. How can I make sure its not on backwards?