Based on your description of the symptoms, I wouldn't dismiss the clutch connection so quickly.

I was surprised to find on my 300E that the clutch and brake share the same fluid reservoir, although with typical German efficiency the takeoff for the clutch is higher than the brake so if your clutch hydraulics spring a leak and drain dry, there's still enough fluid left in the reservoir to maintain the braking system. I know this for a fact because I drove 30km downhill without a clutch recently after a master cylinder failed.

Also, am I right in thinking that the independent brake systems are split front back, not diagonally? There's a clue there somewhere.

And, I know these are probably stupid questions, but have you:

checked the fluid level?
looked for evidence of leaks on the garage floor?
changed fluid recently?

You don't say how long you've had the car but it's old enough to seriously consider overhauling all your hydraulic systems. One of the first things I did when I bought my car was change all the rubber brake lines and change the fluid. Its worthwhile servicing the master cylinders as well because the seals will give up eventually, and they start leaking when hot. New units aren't expensive but you can also strip them down and replace the seals yourself if you're that way inclined.

A 20 year old car, you should probably think about replacing all the fuel and water hoses as well while you're at it. save yourself a lot of grief later on.

good luck

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1987 300e manual 250,000 km (sold)