Ok if the pedal is soft I would figure that there is still air in the line, or as you stated a problem with the master cylinder. As long as the clutch is corect for your vehicle and you replced the clutch disc as it was suppoed to be you really only have the two previously mentioned items that could be causing this. Ideally if you could get your hands on a vacuum pump and vacuum the bleed process will work better. If not you are stuck doing it by pumping up the pedal and bleeding it that way. If you feel that the bleeding has been done suffecient, I would replce the master cylinder. Here is the bleeding process as I have seen. Just too make sure that you didn't miss anything while bleeding the system.
Important: Ensure no air is drawn into the clutch system.