To ensure meaningful replies, it would be best to confirm what model of transmission your car has. The number is stamped on the transmission body, the lip just above the pan, on the passenger side. It will likely be crusted over with grease and oil. If it's impractical for you to look, perhaps someone else will confirm....
I am going to go ahead and answer, as I am pretty sure it will be like the one in my wagon (which was originally in a 240d), a 722.117 or .118 -- in which case it's a vacuum-only controlled transmission (no lever to the transmission from the linkages).
To do what I suggest you will need a vacuum gauge and a vacuum tester, such as a Mityvac.
I suggest you proceed by:
1 - undo the main vacuum line running to the brake booster and measure the vacuum output of your vacuum pump with a vacuum gauge. Sorry I am not sure I remember the correct figure, I think it's anywhere between 18-22 hg? If it's low or jumping (gauge wavers really erratically), you need to replace the diaphragm in your injection pump.
2 - Apply vacuum through the vacuum line running down to the transmission to see if the vacuum modulator holds vacuum. If not, the cap may be leaking.
3 - if all seems good here, move to the whitish/yellow vacuum control valve bolted to the injection pump. This has a spring inside that acts on a bleed valve. Some of these get very tired and the spring needs to be retensioned. Link to DIY:
http://www.benzworld.org/forums/w123-e-ce-d-cd-td/1261744-transmission-flaring-clunking-vcv-diy.html (unfortunately some of these valves are not servicable, have a lock ring instead of the nut shown in the DIY... in this case you will have to get hold of a used valve that is adjustable).
I suspect your issue is lurking in one of these areas.