While not easy or cheap, my suggestion would be to:
1) Run RCA cables from the head unit to a trunk-mounted aftermarket amplifier (multichannel). Don't skimp on the cable quality, and run the cable down the driver's side, because the main battery cable on a 400E goes down the passenger side (possible noise problems).
2) Do not use the deck power for anything! I'd also bypass the stock MB amps.
3) Run new speaker wire from the aftermarket amps to the speakers, but do not cut or modify any of the stock wiring - this will allow you to return everything to stock if desired
4) Replace the dash speakers with Rainbow coaxials. They are the only, and I mean ONLY, 100% drop-in replacement speaker for the W124 dash. The stock rear speakers are fine. The stock door speakers are ok unless you want to plunk down ~$750 for the nifty
Jehnert dual 6.5 door panels.
5) You can use the now-defunct space where the fader wheel is, and swap in a switch to use as a valet switch for the stereo, or control a radar detector, etc as shown
here.
FYI - the "52 watt x 4 channels" is usually rated a 10% THD, the deck is probably more like 10 watts RMS from 20-20k Hz at less than 1% THD. I'd look for a nice 5-channel aftermarket power amp, made in USA (Soundstream, Precision Power, Orion, Rockford, Xtant, etc). Something 25x4 plus 50x1 would be the minimum I'd recommend. Most multi-channel amps have decent built-in crossovers as well. For some photos of my not-yet-completed W124 stereo install, click
here.
HTH,