Your master cylinder has 2 chambers, one for the brake and the other for the clutch. Each with it's own fluid reservoir, they are just under one cap. Each has their own piston actuated by their respective pedal. If it pumped up and then lost pressure on the clutch or bake, then I would suspect a leaking wheel cylinder and clutch slave. NAPA has new ones at very reasonable prices, almost too good so rebuilding is in question. Like I mentioned, figure on rebuilding the entire system, it will save the other walls of the barn.
