I have the aftermarket booster/master located in the stock position with a 3 sp OD trans. There are no clearance problems and everything works fine. 56 through 59 are basically the same. If they converted the clutch pedal to match the MC swing pedal he will have to locate all the original parts to change it back. The stock pedal and related parts should bolt right in if they haven't hashed up the frame too much. If it still has the original through the floor clutch pedal there would be no change to the clutch linkage.
Fred


1956 3100 Pickup/Red/350/3sp OD/PS/Disc Brakes
1957 Bel Air Sport Coupe/Red/355/TH350/PS/Disc Brakes
2017 Silverado LT Single Cab SB/Black/5.3/6 Speed Trans
1947 Willys CJ2A w/F-Head engine