Good day, sir.
Since I am barely qualified to touch a Mercedes let alone make modification suggestions, I will stick to the easier topic of your stereo speakers. Blaupunkt and others make ultra thin 6.9 three way speakers. Ultra thin is a bit optimistic but the mount with a 2.25" depth making them a good fit in a lot of tight places. The speakers might fit into the fender side of the foot well. The passenger side has the hole for the power antenna but I couldn't tell how much room it takes up. The driver side is covered and would have to be cut out. Interestingly, there is an approximately 3" hole down by the hinge pillar with four studded holes around it. Small speakers could be placed there.
Monsoon used to make magnetic planar computer speakers, about .75" thick. Though you would need something to produce low-end frequencies (besides road noises
), a set of those would also work. I don't know if they are still in business but once upon a time I retro fit a set with an iPod, small amp, and a 6AH battery for making a bicycle stereo system. It should certainly work in a car. A quick search on eBay for "Monsoon speaker" turned up a set for $15. The only issue is that they need a powered driver, which means no direct-to-iPod wiring. Polk Audio also makes a thinner set (1.75") in a rectangular configuration that also fit the bill with a better range since they are two-way.
I also kind of like the idea of replicating the wood grille that covers the center speaker and mounting it to the top of the transmission tunnel in a nice little leather covered box, as close to the underside of the dash as possible. Mount two small speakers in one box, with each facing a headrest. Run the wiring under the carpet right up to the radio. It "busies" up that transmission tunnel but the wood grille should appear to belong on first glance. Or match it to the facing of the heating/cooling vents.
The easy answer is to build a reinforcing bracket and mount them in the rear wall. It mean cutting out holes but the rear upholstery covers the hole. 6x9 drivers easily power through the material and provide enough sound to be heard. The downside is that they are visible in the trunk.
The interior is still out of the 280 we are fitting with the 3.5L. I'll take a look at the structure tonight and see if any other ideas come up.