I have been going crazy trying to locate a similiar clunk in my front end.
It almost sounds like there is a bowling ball under the front seats.
I started with the most obvious parts, the shocks, but that made no
difference.  I thought for a second that I had found the source of the clunk
when I noticed that the cone shaped part was missing from the right lower shock
bolt. Adding this with the new shocks didn't help.  Next part that I replaced
were the upper ball joints.  Nope, that didn't do it either.  I finally gave in
and spent an hour of shop time at the closest VW dealer.  He said that it
was definitely upper control arm bushings.  For $650 they could replace them
and add a front end alignment and I would be good to go.  I thanked him
kindly and did the work myself.  About $100 for the bushings and a
remarkably short 2 hours and both sides were like new again.  (I have access
to a mig welder).  The first bump out of my driveway lt me know that that
wasn't it.  The dealers second guess was the outer tie rod ends.  I had just
replaced them less that 5000 miles ago with a rebuilt rack and the inner tie
rod ends.  He says they are the loosest part in the system, I'll
chang'em out.  As I suspected, that made no difference at all.
I stopped going back there. There guesses were getting too expensive.  I can
guess for much cheaper.  The only parts left were the sway bar bushings.  I
don't know who said the doughnut looking bushing slips right on with soapy
water, but mine sure didn't.  I must have spent 2 to 3 hours trying to get
those bushings on, while honing my creative language skills.
Nothing.
I've almost given up.  I'm starting to actually like the noise.
Any suggestions are alway welcome.  The lower ball joints are the only parts
that are original.  The alignment guy said that they are in great shape,
those aren't the problem.  I just don't know where to look anymore.