Seems the SSBC conversion is not a good choice. Recall several other users having problems and could not solve them. Support gave them things to check, do, or replace, and the issue was never resolved. It is even possible you have a bad master cylinder right out of the box.
Power and manual brakes can have a different pin position on the brake pedal under the dash. It changes the ratio of the pedal to provide a different fulcrum and thus a different pressure on the master cylinder. I also believe that the pushrod used for a manual master versus power brakes may be different in length. The manual gives specific stick-out lengths for the power brakes depending on which type manufacturer used.
From my 1968 Factory Manual just to give you some figures, power and manual drum brakes used a master cylinder with 1" dia bore, while power and manual drum/disc brakes used 1.125" dia bore (calipers on the 1968 cars used a 4-piston design so later 1969 and up master cylinder bore could be different). Decreasing MC bore size will decrease your pedal effort and increase your pedal travel. Conversely, a larger bore will increase your pedal effort and decrease your pedal travel. A too large of a bore master will make for a real hard pedal. Learned this on an old truck I am working on and someone installed the incorrect larger bore when I needed the smaller bore for my application.
Pedal height for manual brakes is measured from the underside of the standard pedal pad to floor pan and is 7 1/8," but I have a line diagram using the power brakes and the pedal is closer to the floor with a measurement of 4 1/2".
Make sure you bench bleed the master cylinder while it is out of the car to ensure no air bubbles in the bore's piston.
I don't know what type of disc brake shoes/rear shoes you are using, but if you were sent the "hard" metallic compound that is also know as the "premium" or "lifetime" type, they will not stop well and require a lot of pedal pressure. They work best when hot which does no good for everyday driving. Get a set of the inexpensive pads/shoes which are softer and grab better at lower speeds. They also won't chew up the rotors or drums as fast as the hard material.
Being no brake expert, I found this thread on the internet that may be of some help: Master Cylinder bore size= what is the criteria?
Also found this YouTube video. Don't know if this applies to your situation or not. https://www.youtube.com/watch?time_c...&v=qPLaPv8DITE