Remove the switch until you bolt the pedal up. Then install and adjust the switch (slotted hole). The switch shouldn't interfere w/ pedal motion, just sense it.
The brake pedal doesn't push or pull the MC piston (unless you use your foot). The MC should position the rod w/ its spring and stops. The pedal just goes along for the ride. You only need a different length rod if the pedal doesn't sit where you want it. Ex., you don't want the pedal bottoming out on the floor before the MC hits its stop, and you don't want it sitting way above the gas pedal, unless you drive w/ 2 feet (like I do and they might now teach in driver's ed). Thus, neither rod, nor pedal, nor switch should affect or interfere w/ the "throw". It is common sense once you understand this.