Congrats on your new/first car! Looks like a pretty nice example.
Most of your problems should be covered by the Mercedes-Benz 50-year warranty on everything. j/k, a little hazing for the new guy.
I agree that you might want to keep the overrides, at least on the front, because SUV's seem to have been specially designed so that the towing hitch and rear mounted spare tire match up exactly with your grille and will dispatch it quite easily. The rear ones do look a bit more awkward because there are two sets visible.
I'd check the brackets for the exhaust first, very common and an easy fix, always start with the easiest remedy first. You should be able to get under there and shake it and see if it's tight or not, you may only need a couple of new bolts. Your dash doesn't really look that bad, especially for a dry weather car, but OEM dashes can be very costly tho I'm not sure for your specific model. You can buy a dash pad, some are fitted from shaped plastic that look almost OEM, rather than those carpet type ones that never really look right. I had a fitted one on my old Jag and you couldn't tell it was on there. Uses two sided tape and fits snugly to the contours. Most sedans from any manufacturer don't include key locks on the rear doors, it is assumed the driver will enter the car first in most instances. You will probably need to buy a new handle rather than try to fix the knob, should be relatively inexpensive on eBay, etc.
I just reread your post and the reply before mine, didn't notice you said it vibrates in "D" only, so agreed that it's likely a motor mount or maybe even transmission mount. A common fix and probably could be handled by anyone, but use MBZ parts to save you having to redo it again in a short time. Usually not a safety issue so long as it's not shaking you out of your seat. I leave the rest to the other knowledgeable members here, and congrats again for locating this site, it's a valuable source of information.