I believe there should be a thick rubber washer on the pedal shaft below the floorboard to establish the right pedal height and also act as a dust seal to keep dirt and debris from getting into the cab through the hole in the floor. A good substitute for the OEM washer would be a few pieces of tire sidewall cut into about a 2" washer with a center hole that's a snug fit around the pedal shaft. Cut an angled slot in each washer and glue them together with trim cement after placing them onto the pedal shaft. One of the resto-ripoff parts places might have the original dust seals, but junk tires are cheap and plentiful. Once the pedal height is correct, then adjust the master cylinder linkage to make sure the brakes release correctly with the pedal topped out.
Jerry

"It is better to be silent and be thought a fool than to speak and eliminate all doubt!" - Abraham Lincoln
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