Did you check backlash on the rear-end? If the ring gear is set wrong or has a lot of wear it will clunk. You can do quick check by unbolting the driveshaft from the pinion yoke and see how much play is in the yoke. It should measure between .006 to .010


I'm getting a clunk on my D200 when it's put in reverse but haven't had a chance to look at it.

Ring and Pinion specs