Bled the brakes a few times, it has new calipers, and master cylinder, I have a stiff pedal after pumping a while with the engine off, lose all pedal after starting.. Thinking the proportioning valve may be the culprit.. But not 100% any ideas?
Did this low pedal all start after the m/cyl and front brake work?
Have a helper watch for any brake caliper or pad deflection/movement as you apply the pedal with it running. An 1/8" of hardware, rotor, pad or caliper movement up front may translate into 2-3" of brake pedal movement.
The same can happen with the rear shoes. Be sure that the hardware is in good shape and that the shoe/drum clearance is adjusted up to lightly contact the inside surface of the drum.
Verify that the m/cyl is the correct one by comparing it to the original. The brake booster pushrod (even if it is adjustable) shouldn't need adjusting just because of a m/cyl replacement.
Go by the service manual procedure only if you try to adjust the booster pushrod.