When I had this same problem in my '87 SL, the 'clunk' I was getting on shifts turned out to be the transmission shift modulator. Essentially, it's an adjustable vacuum fitting mounted to the passenger side of the transmission that controls shifting 'smoothness'. The vacuum line that feeds the modulator is the 'main' line that orignates from the rear of the engine manifold and runs to the trans. This line should be checked at the trans end to insure that it holds vacuum. Then using the adjuster on the modulator to increase or decrease, turn it 1/4 turn, then test drive the car. Repeat adjustments until it shifts the way you want. If it turns out that the modulator is bad, a replacement is under $50 and about 5min to install. Virtually any transmission tech can do this service for you; you don't need a Dealer or even an MB trained tech for this.

Re the trans service, remember to drain the torque convertor as well as the trans, install a new filter and pan gasket and a pan magnet should be installed if not already present. The magnet (around $8) serves to collect particles in the fluid.

Pls post how you make out with doing this adjustment, befor getting into flex disks, rear diff, drive shaft etc. In other words, start with the simplest (and cheapest) possible solution and go from there. Good luck w/your car.

Bob

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Bob Jones
Bradenton, FL
'87 560SL-Sold
'99 SL500 For Now