In my 2004 Pontiac GTO the front strut mounts were installed upside down. It took a Pontiac engineer to come out, install microphones in the engine bay to capture the sound, me to reproduce it, and him to find the parts installed incorrectly. I am not saying that is anything remotely what is happening here, but on the GTO they were easy to install incorrectly and when going over a bump unseat and make the clunking noise like you describe.