There are several subtle differences, but the most noticeable is the front calipers. The std calipers have a raised up boss right in the middle of both halves that a single pin goes through to retain the pads. The J56 calipers use a different pad, with the steel plate bent outward at a 90 degree angle, so this raise area isn't present. Instead of the single pin in the center, they use two VERY LARGE cotter keys at the outer edges of the pads for retention.
I'm unsure of the other configurations in other years, but the 67's had a different proportioning valve also. The 69's had a valve that appeared std from the outside at least, but required the J50 power brake option also as a mandatory addition to the J56 option. I've seen one 67 car that I believe to be original with J56 manual brakes.