Hey Matthew,
First you need to be absolutely sure the brakes are adjusted properly. On a total rebuild, I always adjust them up tight to the point I can't turn the tires. Then I power bleed. First through the hydro-vac then the rears, then the fronts. If the pedal is still too low and doesn't pump up, then adjust the pedal to master or booster rod. Not too tight until the shoes get backed off.
Good luck.
BTW, you won't have to remove the cylinders, the air comes out, especially with a power bleeder.
