Bit of a bump from the dead here.
I have adopted mechanics duties on a coworkers '02 MP5.
She is complaining of a rear clunk in the back (similarly described by the OP). The car has about 60k on it. I've driven the car several times and can confirm.
Without inspecting the shock/strut tubes for obvious damage/leaks, is there indeed a history of defective struts on these cars? Does the tophat need to be done too?
If so, point me in the direction of a thread that has play-by-play DIY pictures to change the struts. (ie what plastic interior parts do you need to get to the top hats, O-drive socket set needed, etc)
Subaru's have a similar defect on the STI strut, but it is because of a bad tophat.