Start about going it systematically:
1. Do a compression check
2. Check injection pump timing
3. Check valve clearance and adjust to spec if necessary
4. Check the timing chain for wear and excessive stretch (with the valve cover off when checking the valves)
5. The injectors may be worn out - do a diesel purge first to see if the engine quiets down. If you have no record of injectors ever having been replaced, it's time to do so.
6. Does the engine have proper oil pressure? It can read as low as 1.5 bars at idle, but it should peg out at 3 bar at about 1200 RPM.
7. What is the indicated coolant temperature while driving? Should be 85-90 degrees C.
Does the engine use any oil?
There may be some other sources of engine clunk, such as worn piston pins, etc.
The No. 1 Source for Mercedes DIY Manuals, Repair Kits w/ Instructions and OE Parts New and Used | MercedesSource.com has a good booklet "Why does my diesel rattle and knock?" This may help you pinpoint the problem.