I reckon that the new master cylinder you have requires a longer rod (the one pushed by the brake pedal) in order for the 'pistons' inside the MC to travel through their complete length.
In other words, the rod is not long enough to push the piston to the end of the bore inside the MC, so you are not getting enough pressure, particularly to the front calipers, and it will also mean that you will never get all the air out of the front brake lines.