OK, you might need a new MC, but maybe not. Here is the situation. If that were a single chamber MC, and you were hooked to only the front brakes, then it would be obvious what the problem was.
Hydraulic fluid is not compressible. If the calipers needed 1 ounce of fluid for full travel, and your MC put out 2 ounces at full stroke, then your pedal would go down half way.
If the situation were reversed, then the pedal would go down all the way and the car would not stop.
But, in either situation there would be no sponginess.
But, in this case, you have a dual system. There are two pistons in the MC, with springs between them. Its possible that the rear system piston is stopping its travel when the rear brakes start working, but the front system piston is still being moved by the spring which is the spongy part you feel.
I did not explain that very well.
If so, then you will need the bigger MC. Just remember that a bigger MC normally causes a harder pedal. But, in this case, the calipers are larger also, so it may be harder than it is now, but not abnormally hard. Of course, the brakes are boosted, so you might not notice any difference.
But, if you have access to a power bleeder, or the urge to build one, I would power bleed the brakes first.
An air bubble in a high spot in a line can stay there no matter how many times you bleed it with the MC.
If the volume of the fluid in one stroke is not enough to push that bubble past the end of the high spot, it can move back up while you are closing the bleeder, letting the pedal back up and then going again.
In which case, it just moved up and down and never goes out.
I have seen more than one system that had had gallons of fluid bled through it that only lost the spongy after a power bleed.
BTW, if your MC was more than a couple of years old, and you bled the system by opening a bleeder and letting the pedal go all the way to the floor, odds are you need a new MC anyway.
After a couple of years or more of driving with the piston going back and forth in the same part of the bore, crud and rust will build up in the unused part.
When you shove the piston where no piston has gone before, you scar the heck out of the rubber seals and it goes bad shortly.
Also, I assume that the calipers are not upside down. On many of those axles, you can put the calipers on the opposite sides.
They fit and work just fine, except that the bleeder screws are on the bottom. You will never get all the air out that way, unless you turn the truck upside down. Not necessary an unlikely event with this bunch...........
I figured because the stock one worked with my 3/4 ton swap, it would work with this, but makes sense I might need a new master cylinder. What should I use?
I doubt if the fluid on this truck was EVER changed. 
That sh!t was like molasses. 
