Seem to have some trouble with rough shifts in lower gears (2-3, 3-2, possibly 3-4 etc.)

When accelerating slowly, you can feel the car "disengage" the lower gear, RPMs drop, then reengage the higher gear. Thump and thump.

When taking your foot off the gas, there is often also a weird thump. Not sure whats going on. This is all in C mode too.

Only had the car for about 3500km (has 54000km on it). Didn't seem to do this before (in fact, before this started I couldn't even detect shifts except by the tach).

 

Two things - change the fluid and get the TCU flashed with the latest software. MBZ recommends the transmission fluid and filter be changed at 60,000km's (and most experts agree it should be done every 60,000km's/39K miles). I just changed mine a few weeks and ago, and at 39K miles and it was absolutely black. I also had an issue with a rough 1-2 shift over the winter when it was cold and my dealer updated the TCU code and the whole transmission shifts like new now.