Unfortunately stiffness in a "Sports Oriented" vehicle is a must. This complaint has popped up a few times over the past few years over at the W212 forum. I don't mean to say that people don't know what they are buying, but, in many cases, people fail to understand that "Sports Suspension" = Stiffer suspension. In order to make cars "handle", some sacrifices need to be made in the form of comfort. Soft suspension = more comfort, but that ALSO = less handling. Anyone ever rode in a 1980's Town Car? It was like floating in a cloud.... trying to make quick maneuvers at less than ideal speeds would make you feel like the car was gonna flip over. You can't cheat physics. As stated above, it's the car. Best you can do to alleviate the harshness is to (again, as stated above) set to comfort mode, make sure suspension is set to softest (no lights on), do a lil research on what tire offers the most comfort (I see you are already running AS tires, which are usually softer than Summer tires). A few did mentioned that the Non-AMG E's rode much better/softer than the 63's (which I totally believe even when I have never ridden in one).
As for your interior squeaking. You first need to determine what exactly is making the noise. It could be something as simple as one of the trim panels is loose. Next time you hear it, try pressing down on the possible culprit and see if it stops. Maybe it can be popped back in or re-tightened. Wish you luck finding the squeaking part!