pedal travel help needed

Here's what I would do. With the lines in the MC loose, so the pedal can go to the floor, push the pedal to the floor while you're under the dash and hold it all the way down. Now get a black sharpie and put a reference mark on the MC pushrod even with the back of the MC bore where the pushrod enters the bore. Now turn the pedal loose and disconnect the pushrod from the pedal. Now push the pushrod buy itself into the MC as far as it will go and see if it goes in further referencing the mark you put on the pushrod earlier. If it does, you're not getting the full stroke from the pedal to the MC and the rod needs to be lengthened.