Tuts59,
I still don't see a problem with the clutch linkage. The clutch and brake pedal on my 56 do not share a common shaft. I recently replaced a stock MC on a 59 and it had the same configuration as my 56 before I converted to disc brakes, booster, etc. The only thing that has been changed from stock on your truck is the additional length of the clutch adjustment rod because your engine is moved foreward. The aftermarket Booster/MC kits mount to the existing MC holes. They also come with a replacement pedal pivot pin. I have installed several of these units the most recent a 55 3600 using a 8" dual diaphram booster with a dual MC. It has a warner 3 speed trans which is a large unit. I have a similar configuration in my 56 with a 350 V-8 & 3 speed OD trans. There are no clearance issuses on either application and no interference with the stock clutch linkage. Take a look at the kits offered by ABS Brake. www.abspowerbrake.com.
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