Found this on Sabbnet but it does not indicate if changing the MC fixed the problem. This is an exact description of my problem.
1999 95 SE 4 cyl, I Have a braking issue. The brakes stop the car, however sometimes the pedal will go almost all the way down to the floor board. When I pump the brakes once its fine. Usually this only happens when I'm driving on the freeway and have not been using the brakes for 10 minutes or so. When I'm on the brakes quite a bit theres no problem.
My first guess was calipers, but I'm doubtful of that now after examining the pad and rotor conditions. I'm thinking this may be a master cylinder issue, or possibly air in the brake lines. Before I take any steps I am wondering if anyone has experienced this problem.