[Quick Toy]

I went through a similar problem when I put in my Ford 9" with a rear disk setup. I had to do a bunch of math calculations to get the pedal force correct.
Because the cylinder volumes are different from the old drum hydraulic cylinders and the new disk caliper cylinders, the bore and stroke of the master cylinder needs to be matched to the new setup. Usually with the increase in the volume, now required with the rear calipers you need to go to a smaller bore master cylinder. (I know it sounds backward but remember you are dealing with area and pressure)
Sometimes you can find a similar master cylinder from a 4 wheel disk brake car, that may work with what you have, or you need to do the math and see what comes close swap wise.
(Remember that there usually are two pistons in the master cylinder. One is for the front brakes and the other is for the rear. The placement of the seals on the pistons will have an effect on the volume delivered. Hence, disk/ drum setups and disk/disk setups.)
(I ended up using a master cylinder off a 4 wheel disk 280 ZX. that had the correct bore and stroke for my setup. It was mated to my stock brake booster.)


FWIW
I had a hell of a time bleeding the brakes, thinking I had gotten all the air out of the lines, but the pedal still felt spongy. I got a tip from a old school guy, who told me to hold the caliper with the bleed screw facing up and lightly tap the caliper body with a hammer to free the bubbles that got stuck around the piston and bore...Worked like a charm, and a bunch of more air came out when I bled them again.


HTH
Paul