As for what you did wrong, best guess is that you're running front calipers in the front and rear of a short wheelbase, high CoG rig.
That said, I have a few questions:
1. What is the piston diameter of the front calipers? Or year/make/model you bought them for? The assumption is a 2.94" piston diameter with 6.79 in^2 effective piston area, but there are large piston variants of those calipers that are otherwise identical with respect to mounting, brake pads (FMSI D52), etc.
2. Same question for the rear calipers...what are they?
3. Front rotors are presumably Ford Ø11.72" x 1.20", so what rear rotors are you using?
If I assume that you're running 1987 or older 3/4-ton GM front calipers in the rear, as opposed to parking brake calipers, then most likely the biggest issue you're facing is that the master cylinder bore size is insufficient for the given caliper piston area. Front calipers up front, no biggie, but front calipers front and rear can be an issue depending on caliper piston areas. While stepping up to a larger bore master cylinder should fix your pedal issues (nvrstuk had similar problems on his most recent build updates), it won't do anything to address the front/rear bias problem.
You can add an adjustable proportioning valve in order to try and reduce the rear brake bias slightly per what Paul said, however those are not meant to overcome a major component mismatch if that is indeed what you have and would not do anything to address your pedal issues. Instead, you could swap out the front calipers in the rear for the parking brake caliper equivalent as offered on the 76-77 Cadillac applications, which have smaller piston areas (Ø2.03") and would reduce the rear bias accordingly, as well as the fluid volume requirements, making the 1.125" bore MC more suitable for the application.
If you choose to stick with the calipers you have, like you indicated, then I'd suggest that you run a bigger bore MC and deal with the premature rear brake lockup and over-steer condition it creates. Your best bet at that point might be a front/rear friction stagger to reduce the rear brake torque to the point that it's at least safe to drive in a panic stop situation. Higher CoF up front, lower in the back...see where you land. Adding an LBS type of valve could help band-aid the situation further.
As for line size, that has nothing to do with anything really. The MC determines how much fluid is supplied to the front and rear brakes based on the bore size since we assume brake fluid to be incompressible, and the line size just carries the fluid. The only thing line size determines is fluid velocity, and to a certain degree, system compliance since larger lines expand more under pressure than smaller ones.
Last but not least, you could convert over to a dual master cylinder setup where you could stagger the MC bore sizes to match the calipers, since the relationship between the master and slaves (calipers) is important.
HTH,
Tobin