-do you have the valve oriented properly? the port for front brakes actually goes to the front brakes etc? if backwards it may cause issues.
-do you have the master hooked up properly, front brakes are hooked to the correct port etc? is your master cylinder made for disc/disc?
-maybe a faulty valve? they work by limiting brake pressure to the rear brakes so it kinda makes sense if it is faulty there could be limited brake application.
-does the pedal bottom out or does it stop at a decent height but still no rear brakes?
-is the pedal geometry and pedal free play/booster pushrod free play to master cylinder correct so that the master cylinder is getting a full stroke and allowed to return fully when released?
--do you have a frame mounted booster/master cyl? residual valves? some master cylinders have them built into the outlet ports and if your system uses a rebuilt master cylinder you may have obtained one that was originally set up with residual valves in the outlets of the ports, or possibly just one port, for front and rear drum brakes. that could be holding a residual pressure in one circuit so one circuit would possibly require less fluid until they bottom out the pads and build pressure. the other circuit may not be at the same point.
-could the prop valve/combination valve be distorted internally from over torqueing the lines, causing a binding inside?
-do you have a switch terminal midway on the valve, if so, when tested does it show as "turned on"? that would indicate the piston inside the valve has moved, like you have lost brakes to one of the circuits or like you have one of the circuits that has flowed significantly more than the other, so the pressure differential has moved the valve, which would explain your issue of not much brake action to the rear. a "fast bleed" on one of the circuits (rear)may trigger the valve to move which basically shuts off a circuit. there is a link to a site explaining the prop/combi valve with a drawing of the internals.
-have you checked the operation of the brake booster? could the atmospheric valve be faulty or the filter be blocked somehow? does the pedal return fully, is there a built in stop to ensure the pedal returns to the same position/height each time?
-did the system ever function properly? when you say you have a nice firm pedal with engine off, do you also have solidly applied rear brakes as well?
-can you explain what happens after a few pumps of the pedal, engine off. then after the engine is started what does the pedal do? if a hard pedal, if you hold the pedal at a constant pressure, does it slowly fade to the floor? this would indicate an internal leak in the master cyl.
-if you were to look into the master cyl reservoir while a buddly stepped on the brakes, is there a disruption of the fluid at first, like a small fountain of fluid is pushed back into the res, and then with more pedal travel the disturbance goes away and brake application starts? this is because the piston in the bore has to travel back past the cylinder refill ports, when the brakes are released, which allows fluid to replenish the bore as fluid is used or allows extra fluid in the system, caused by heat expansion or whatever, to return to the res. if there is no little fountain at first application of the pedal then maybe the piston is not returning fully. this can be a pushrod travel adjustment between the booster and master or between the pedal and booster or possibly simply because there is no pedal stopper so the pedal height is allowed to change. a changing pedal height can mean the brakes work differently with each application because the master can sometimes not be allowed to return fully.
https://www.motor.com/magazine-summa...nder-selection
https://m.roadkillcustoms.com/test-power-brake-booster/
https://www.freeasestudyguides.com/b...operation.html
https://www.classicperform.com/Instr...akeLineKit.htm
http://mbmbrakes.com/proper-brake-system-plumbing/