Hey dude,
Very old thread haha!
But yes, I had this problem, when I first got my series 2 I had an annoying clunk coming from the rear of my car.
It turned out it was my standard muffler knocking against the under body, but it would only do it after it had warmed up!
As soon as the exhaust was changed it is quiet as. So thats one thing u can check if you still have the stock exhaust.
Also as mentioned earlier in this thread its worth attacking the standard suspension with a socket set and making sure everything is nice and tight.
Hope you can fix this mate, It used to drive me nuts!
Seeya!