I was reading in the SLK forums and the guys who have the 6 speed manual say that it is the best manual transmission that they have had. Particularly the SLK350 manuals. Take a look--they love them. This would probably be my first choice.If you don't like the auto, you're going to hate the manual tranny. MBs manual aren't nearly as good as their good automatics, nor are they as much fun as say a Audi or BMW manual tranny.
The manual boxes in the W124 were very numb, and with a diesel the experience is even less pleasing.
As far as using a auto box from a V8 W210, the answer is no due to being fully electronic with gear selector module, etc, etc, etc.