I too am having trouble right now with my '06. I had a pinion seal leak at about 2.4k and the clunk started about that time as well. Dealer said it was normal.

Now at 23k, I've had a second pinion seal leak, shifting is very difficult and it has the low-bass noise associated with clutch pack failure. Dealer still says it's normal and that it just needed the differential oil changed.

Unfortunately the next closest dealer is 60 miles away.