Two things you seem to be concerned about. 1) you believe the booster is interfering with travel.
2) you believe there may be a master cylinder issue.

To test #1, unbolt the master cylinder from the booster and step on the pedal to see if the pedal will travel all the way to the floor. If the pedal does not reach the floor, your issue is in the booster/pedal assembly. The vacuum assist of the booster is only an assist, meaning there should still be a mechanical connection and you should be able to overpower a defective booster with pressure on the brake pedal. Without a master bolted to the booster, the pedal should push to the floor fairly easily and smoothly. Get an assistant and measure the amount of travel the rod in the booster travels from pedal completely up, to pedal completely on the floor. If the pedal and booster operate correctly, reattach the master, and move on.
2) Now you have to determine if the master cylinder is the cause of your issue. With the master reattached to the booster. Loosen both brake line connections and see if the pedal will still go all the way to the floor. If it does, the issue probably in not in the master. It is possible the master plunger is not completely returning all the way to the back stop of the master cylinder, upon brake pedal release and it is not refilling with enough fluid to reactivate the brakes. If you tighten the lines you loosened for this test while the pedal is still down, you will not pull any air into the system. Once the lines are tight, you can remove the master from the booster to see if the plunger has returned fully to the back stop. I've seen corrosion build up inside the master that will not allow the plunger to return to the back stop and that can cause an intermittent poor brake function. Sometimes the rod between the booster and the master is too long. That will also cause the plunger to not return all the way to the back stop and cause poor brake conditions. If the rod is too short, it will not allow the master cylinder plunger to push enough fluid out of the master to reach full brake pressure (that could cause the pedal to stop before the pedal reaches the floor.) If you suspect the rod may be too long, you can add a couple washers on each stud between the booster and the master and see of that makes a difference in brake quality. If adding the washers does not make an improvement, remove them. The rod between the booster and the master is adjustable, adjust the length in or out 1/4 turn at a time (a little makes a huge difference). If the pedal reaches the floor with the brake lines on the master loosened, and the master's plunger is returning to the back stop, the master is not the problem, and we move on to the proportioning valve.

For a few years, the proportioning valve actually would block off fluid flow to one side of the valve or the other in the event of a line failure. Unfortunately, it would also do the same thing while bleeding the fluid if the bleeding process wasn't done easily. The process to recenter a shifted proportioning valve is not difficult, but requires a gentle touch. To test the valve, loosen either the fitting for the rear brakes, or the fitting for one of the front brakes, and step on the pedal and watch the fluid flow. Tighten the line, and loosen the other line (one line towards the front, and one line towards the rear) and step on the pedal and watch the fluid flow. If either the front or the rear line has little or no fluid flow, the proportioning valve has shifted towards the side with little on no fluid flow. To recenter the proportioning valve, you have to open the side with the fluid flow, and bleed off the fluid until you hear the pop or snap inside the valve, and immediately close off the line, and release pressure. Gently stepping on the pedal should leave the valve centered, and the brakes should be much better.

You have been messing with these brakes too long. Start at the beginning, and work through the process to this point and lets see what you have. Gene