so where in the car is the clunk?

Front (underhood)

Middle (transmission?)

Rear (rear differential)

I fear for your transmission. I saw the brown fluid out of my 2007 with 107,000 .... it really needed changing, What I think really needed changing was the filter and that is part of the plastic pan. Not hard to do, but a job to clearfully do with the right (expensive) fluid.

With the X5 level, I could only drain like 4liters of 10 in the trans so I replaced 40% of the fluid. My plan now is to replace that 40% every year (as I like drive about 6000 miles on that car a year) ... til I see it run cleaner and replace the pan-filter somewhere between 25,000 and 50,000 miles.

FYI my biggest prayer for the x5 is that it's transmission does not fail on me.