The transfer case shouldn't clunk when stopping, but some noise(more of a feeling) is normal. Like Benzmac said the lower steering bushing can cause the squeak.
Possibly air is trapped in the hydraulic system of the 4-Matic system, there are 4 different places to bleed after any repairs are made.
Since the car starts out in 4-wheel drive up to 12mph every start possibly the trans is making the "noise"
MERCEDES BENZ MASTER GUILD TECHNICIAN
ASE MASTER TECHNICIAN
27 YEARS M.B. TECH