Granted it is a different model, but I had a sporadic thumping on my 83 300D. I ended up replacing the center driveshaft bearing and mount. In your case I would suggest checking out the center driveshaft bearing and replacing if necessary. I would also replace both flex discs (with new bolts) and the new transmission mount. I know you said the flex discs and such look great, but..............

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2012 Mercedes ML350 Bluetec 91K (hers)
2005 Corvette 55K (fun car)
2002 VW Jetta TDI 231K (mine)
1998 Volvo S70 T5 Turbo 196K (kids)
1994 Ford F150 4WD 249K (firewood hauler)
1983 Mercedes 300D 376K (diesel commuter)