every performance brake upgrade has a break in period it's usually around 300-400 miles of urban driving. This is easy braking miles, like slowly coming to a stop and putting easy presure on the pedal(you can do emergency braking if needed) this allows the pad to bed into the rotor.
did you upgrade to braided brake hoses? If so they are going to offer a stiffer pedal over the rubber brake hoses. the rubber hoses expand when the pedal is applied and pushes the fluid the braided hoses give a more positive brake feel. If the car wasn't stopping, pulling left or right under braking, or the pedal is going to the foor I would think everything is okay, if not you may have to give some more info.