I read most of this thread and didn't see anything about the rod that goes in between the power booster and the master cylinder. I had the same problem with the brakes on my '62.
Take the master cylinder off and look at the power booster. There will be a rod (the one that goes thru the firewall and attaches to the clevis pin that is attached to the brake pedal). That rod pushes on the master cylinder piston. There shouldn't be much play in the end of the rod and the master cylinder piston. That was the problem I had. I wouldn't get any brakes until the pedal was almost to the floor. I had replace the ENTIRE brake system, like you did, and couldn't figure for the life of me why I didn't have brakes.
That rod length is important. Consider where the fulcrum point on the brake pedal is and you can see that a small difference in rod length will translate into a large amount of pedal travel. There should be very little 'play' between the power booster rod and the master cylinder piston. Mine had a rod between the two and apparently during re-assembly it didn't get put back. I ended up making one. Measure from the face of the power booster to the rod in it (the one coming from the brake pedal). Then measure from the face of the master cylinder to the end on the master cylinder piston. The rod that was missing from mine was the one that took up this gap (add the two measurement together). I made a rod this long and then added a dimple in the end that contacted the power booster rod. (the rod from my master cylinder had a radius on the end).
I attached a sketch, hopefully it helps.
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