It may well be the master cylinder, but have you checked for the obvious yet - anything blocking or binding on the pedal or return spring?
The pedal linkage on my 2001 is quite unique compared to any other car I've owned - it is an aluminum truss-style part (stong and weight-saving) with lots of openings that could hang up on something. A footmat or other item that could possibly have made its way up into that area could easily bind the assembly.
Grab a flashlight and take a peek up under the dash and you may find something obvious. While you're down there, check the ease/smoothness of depressing the pedal and something may come to light.
Good luck.
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2001 Lapis/Black/Black, PSM, Rear Speaker Kit, Optima...
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