How much travel does the rod going into the master cylinder have? Generally speaking a pedal ratio of about 6:1 should be adequate, depending on the size of the master cylinder. One other thing to check is if the residual valves are installed correctly, there is an in and an out side to them. Was the master cylinder bench bled before it was installed. I don't mean to be insulting with dumb questions, but often the easiest things are overlooked and can cause major problems.