For various reasons unrelated to the clunk, I replaced the entire suspension, driveshaft, & differential in my '87 300D. As far as I remember, it still clunks when I shift into gear. It just got out of the body shop from a run in with a deer last month and I'm going to replace the engine and trans (head issues). Maybe the tranny is causing the clunk.
To this day I lift the rear of the car with the dif, slip jack stands underneath the jack points, and lower the car. Sure the diff mounts stretch doing that. But from what I'm seen they are a lot more likely to rot from time rather than jacking up the rear of the car under the diff.
I've found it easy to put a 12 mm hex driver in one of the diff bolts and torque on the bolt. If the entire diff clunks around and/or the mounts look shot, they should be replaced. The tool is a must unless you are real handy with a torch
If there's only a clunk from one side or another then sumpin is prolly loose. When I bought my car the PO installed new bilstein comforts and the bottom nut on the passenger shock came loose leaving it to clunk around in the control arm. Other possibilities are badly worn suspension links.