First check to do is unhook one rear brake cylinder and push pedal to see if fluid is getting to the rear. If it is likely something wrong with rear brakes. Not a good idea to use a MC with a smaller diameter than original as this increases pedal movement.
IMHO most likely cause of problem is rear original lockheed brakes need to be adjusted correctly before bleeding and shoes arced to the drums otherwise you will never get a pedal. IMHO I'd junk them and buy repop lincoln bendix brakes which is what I did.
Did you bench bleed the mc before installing? You also need front/rear residual pressure valves. Link shows the components for system on my 41. Message me for phone number if you want to discuss.
I used:
aluminum remote Fill corvette style 1" Bore 4 Port Master Cyl from No Limit Engineering
proportioning/brake light switch valve
residual pressure valves
metering valve so rear brakes come on first
The remote fill MC helped in that there wasn't enough room above the MC or MC interfered with frame in the 41.
Did the same on my 36 that I sold except for the remote fill as pictured with bambalino blue sheet metal. My 36 rusty MC convinced me to go aluminum with the 41
I bled mine with a MightyVac system, works great:
https://www.skf.com/mityvac/products...870/index.html
https://36fordwoodie.weebly.com/earlyv8discs.html