Having read through this thread I assume you are referring to this thumping problem on the 4-matic TE in your signature?

If that is true and after you have eliminated the suspension system as the source of the thumping problem, you may be experiencing an issue related to your malfunctioning 4-matic system!

The 4-matic system is a consumer of the same hydraulic fluid pressure supplied to the SLS system. There is a unit under the vehicle with its' own separate accumulator and a pair of solenoid valves which actuate the 4-matic mechanics by directing fluid pressure to engage and disengage the components. This valve unit is controlled by the 4-matic controller but you might to able to do some diagnosis by piggybacking say a 12V LED indicator to the solenoid valve leads and observing if there could be any electrical signaling that may correspond to the thumping. You may be able to ascertain the same by simply getting under the vehicle and putting you finger on the solenoids and feeling if there is action that corresponds to the thumping.

Alternatively, by inserting a guage into the hydraulic fluid system it would allow you to observe pressure fluctuations if that is the source of the thumping, this would be somewhat more difficult and require fabricating or finding the guage and connecting parts to accomplish.