Did you bleed the master cylinder before putting it on? If not and its on the car. What you do is make sure the resevoir is full then pump the brakes and then hold the pedal down. Loosen one of the nuts coming of the master cylinder a little until the pedal is able to be pushed to the floor and ait or brake fluid comes out. Make sure you have something around as it could cause a mess. Bleed the master cylinder just like when you bleed the wheels. Do this with both the front and rear lines. When you have bled the master cylinder continue to do each wheel. Even though you had not taken the brake cylinders off the wheels you will need to do each one to make sure the air is bled out.