How is the pressure of fluid when you are bleeding the brakes? Does it not start moving until the second pump, or do you get fluid coming out immediately?
Also, did you bench bleed the master cylinder while level outside of the car, before sticking it in there?
Were the brakes in the rear properly lubed and adjusted when everything went back together?
Are they still adjusted properly?
Where did the master cylinder come from, and was it new or remanufactured?
I think the booster just manages braking assistance, and has nothing to do with the actual creation of pressure. While it may be an issue, it may also fall right in line once the pressure issues are sorted out.