if you don't have a positive pedal stopper in place i suggest to install one and I would also suggest one that has a small rubber or urethane bumper but not too much depth on the elastic part because that may wear in and cause the pedal height to change a little. a positive metal on metal stopeer could be used next to the elastic one I suppose. the elstic one would stop the "thump" and the metal one would stop the pedal at the same place every time. originally the pedal arm may have had a rubber block on the pedal arm which bottomed on the firewall.floor. I remember that noise when driving with my dad in his 59 apache, especially when starting on a hill.
for the booster to master pushrod clearance I would suggest to look at the astro van and see what the booster is supposed to have, same for the pedal to booster pushrod.
most frame mounted systems with disc brakes usually use a 2 lb residual valve in the systems so the brake fluid doesn't run back to the master cyl.
https://www.parrautomotive.com/index...at/cat1911.htm