"Takes two pumps of the brake pedal to get good brakes."
You will be thoroughly bleeding the brakes after replacing the master cylinder, then "set up the brakes", and I think that problem will go away. Don't forget there's a bleeder on the hydrovac.
There's different size mater cylinders because the brake slave cylinders at the wheels vary in size, as well, due to axle weight rating variations, or maybe who made the particular axle/wheel/brake setup used on your specific truck.
Also, it wouldn't be uncommon for the hydrovac to be leaking brake fluid, either, into the engine's air intake. Take the vacuum hose off of the hydrovac and note if there's any wetness/brake fluid inside of it.
Also, it's a good time to check/clean/replace the hydrovac exhaust filter, likely cleverly hidded up behind the driver's step, or possibly behind the seat.