What it looks like you have is a manual brake master cylinder with an insert installed to take up the space to the booster pushrod. Not a problem, but I haven't seen that before.
You also have a combination valve, and if I understand you correctly that is the same one that you used when it was disc/drum correct? If so, that is the wrong unit for disc/disc. Did you remove the drum brake check valve out of the combination valve, out of the master cylinder (some masters have them built in) or was it an inline valve?
What I would do is this. Disconnect your brake pedal from the booster so it isn't pushing against it at all. Put that spacer into the master cylinder, lengthen the pushrod coming out of the booster quite a bit. Then, slide the master onto the booster and you should feel the piston hit the pushrod. If so, shorten the booster pushrod and retest until you can just slide the master onto the booster without feeling resistance, then shorten it about 1/2 turn more. That way you can be sure the booster isn't preloading the master, and that there isn't too much clearace. Bolt on the master cylinder to the booster. Then, adjust the pedal pushrod until you get the pedal height you want and tighten the jam nut.
Now is where it gets interesting. If you like, bleed and test the system and see if it is any better. If not, remove the combination valve and set it aside. Install a 2lb check valve, one in the front lines near the master cylinder, and one in the rear line along with an adjustable proportioning valve in the rear line, bleed and retest. I think then things will be much better.
I still would like to know what kind of calipers you have on the rear axle.