At the risk of oversimplification... could there be insufficient vacuum? What about trying the old master cylinder as a test? Once again, not trying to insult your skillset, but did you "bench bleed" the master cylinder first?
If the pushrod is at the shorter setting, I would guess that it lessens the travel, and therefore the master only actvates the front circuit?
I had manual 10" drums on my 70 Charger when I got it. I converted the front to power discs from a 75 Dart... Booster, brackets and everything. Now that I have the MP 509 cam and its piss poor vacuum, I am considering a manual disc setup. Sure, if your car is original I could see wanting to retain the booster, but you do have options if the power stuff cant be tuned to work properly.