It could be a couple of things. The master cylinder piston recess could be shorter, causing the increase in pedal height. The pedal push rod then makes the pedal stick out further. Take a look and see if there is an adjustment for the push rod (threaded). If the brakes are working well, then just adjust the rod to get the pedal where you like it. If the rod is not threaded, then look at Classic Industries for an adjustable rod. If your brakes are not working the way you like, then most likely the cause of the high pedal is related.
FWIW, I have a 1970 Super Bee. I have converted the brakes to 4-wheel disc (Wilwood). Yes, it's not cheap, but it's a ton better than what came on the car. Good luck, ord27.