The rod between the master cyl. & booster may be too long not letting the piston come back all the way. You either have air in the system or the shoes are not adjusted up. You emergency brake may be too tight pulling the rear shoes off the anchors. I think I nwould snatch off the MC & bench bleed it making shure you have pressure at both outlets. Like Stuart says the pedal should be real high with out the vacuum & drop down some when you start the engine.
