You need to be absolutely sure there is no air in any of the brake lines, and make sure the calipers and pads are operating freely. You should use a pressure bleeder, or other type that prevents the brake pedal from being depressed, this can cause damage to the master cylinder and give you the problem you are experiencing. Also, different pads have different stopping ability, and the rotors should be re-surfaced before replacing the pads. If the new pads are used on rotors that don't have a flat surface, you can experience a low pedal as well.