Long Travel Soft Brake Pedal

My 2cents.
C-clamp all the pistons into the bottoms of their bores, then pump up the pedal, then let the pedal normalize, for several seconds. If you now have a high and hard pedal, then you do not have a hydraulic problem.
Now you can chase the real problem,
which would then be mechanical; maybe flex, misaligned calipers, twisted brackets, or things bending which shouldn't be.
Attack the rear first.
The way that the M/C is designed, If the rear has excessive travel, then the rearmost Power-Piston in the Master, slides on past the rear port until the front Power-piston reaches hydraulic lock. That's a lotta pedal travel right there.