I would say have as much sticking through the floor as you can. On my 34 Ford the brake pedal actually hits the bottom of the floorboard before it begins the bend to enter the car. After you have your system plumbed and have bled it you will have a better idea of how much to have sticking through. If it is too high inside you can adjust the master cylinder actuation rod to lower the pedal. You do not want is so low that it prevents you from applying full braking force.