Most likely what got you in this situation "in the first place" was the previous owner's maintenance habits. Who exactly said that the brakes "were not up to the rest of the car from the factory"? Speaking from personal experience of driving ALLOT of these cars I'm not sure your car is "up to snuff". As Benzmac can testify, the brakes on my 400E stop to the point of brutality. They are "only" the updated OEM's. I've flushed the fluid and kept the rest of the system functioning as it was designed to. Whether the rotors are a bit "dished" and hence have more surface area, or some other thing I'm not sure. If that is the case it is VERY slight. My particular car will outbreak nearly anything but a Porsche 911.
After driving literally dozens of these cars the areas that are not up to par in my opinion are the wheels/tires, transmission refinement of the 4-speed, and (in the 400E's case) differential choice. Some newbies gripe of the climate control, but it works great once you get used to using it. Everything else is truly world class even to this day. Lexus highly touts its "variable valve timing" in its latest cars...so what! The M119 V8's had that as far back as the 90 model year. (in the SL500) The item on the W124 4.2 cars that is the most lacking is the rolling stock. (wheels/tires) C'Mon Mercedes, what gives with putting 195/65/15 touring rubber on something with 300 lb-ft of torque, nearly 300HP, and weighing about 3600-3700lbs? We know you know better... Considering that size is more common to 120HP Hondas and Toyotas that weigh closer to 3000lbs. Great engine, great chassis, top notch suspension design, ditto on the brakes, why impair the rest of it with the inadequate tires? I would recommend 16x7.5" wheels with 225/50/16 rubber. That size works very well and allows the car to use the qualities it has to their fullest. If you never have to drive on snow I'd recommend a set of PZeros or MXX3's. One notch below them would be the Dunlop 8000/9000's and SZ50's. The 50 series sidewall gives you the handling without being a pothole liability or beating the crap out of you over rough pavement.
Each to their own...Lee