Do they pump up?
When its running and you pump the brake peddle, if you keep pumping, will they eventually pump up? If they do, I'd imagine that you lose the pressure after a minute or so and the peddle will go to the floor when you step on it. The system probably acts like a bad master cylinder, which is why you replaced it and the booster.
I am guessing on that base on an experience on a friends rig. He put rear shoes and front pads on everything looked fine. He did a routine brake bleeding and line flush. Went to test it and the peddle went to the floor, barely stopping the rig. Found that if he pumped the brakes three or four times, he could retain enough pressure to make the brakes work. Thought he got air in the lines and blead them again. Got a little air, but not enough to cause a problem and still had the same problem. He then rebuilt the front calipers and rear wheel cylinders, which meant that he had to take the rear shoes off again. He noticed the adjusters were screwed all the way down and were frozen. He freed and lubed them thinking they rusted together because he forgot to lube them after cleaning them on the first brake job. Put everything back together, blead the brakes and had the same problem. He then replaced the master cylinder and adjusted the ball on the booster rod, bench blead the master cylinder, installed it and blead the brakes again. I grabbed my power bleeder thinking that he wasn't doing a good job. No air, so got to thinking that for some reason the slave cylinders (front calipers and rear cylinders) were requiring more fluid than the master cylinder can give. Now the front caliper pistons don't slide far enough back into the bores when the peddle is let up. This puts the front brakes out of the equation. But the rear wheel cylinders will because of the return springs on the shoes. So I pull a drum off and found that the adjusters were screwed all the way in again. This meant that the rear shoes had to move quite a ways before they would touch the drums and that extra movement required the pistons to move quite a ways. That extra movement required more fluid than the master cylinder could give and the peddle went to the floor. I swapped the sides the adjusters were on and the brakes have worked fine ever since.
All that work because of a stupid adjuster.
If it ain't broke, I can probably still fix it.