You need to eliminate the things that are good from the process.
If the plunger on the master cylinder returns back out smoothly, the master is OK. If, however, the plunger comes back out in steps, or stops/delays a few times, the master may well be the problem.
The brake pedal is also pretty simple to eliminate. It either swings freely when nothing is attached, or it doesn't. If it doesn't, find out why before you go to anything else.
If the master is good, and the pedal is good, you have a linkage issue.
When the rod that goes to the master is bolted to the pedal, it should also move freely on the brake pedal (some have a rubber "O" ring the won't allow them free movement, but they will still move without a bind), within the limits of how it can move. That rod should also move in alignment with the brake pedal. If it moves at a different angle, you need to correct that.
Unless you have an added pivot lever, about the only thing left is the rod's alignment with the recess in the master. Some minor up and down misalignment is OK, the pivot of the rod on the brake pedal will accommodate some of the up and down, what it wont accommodate is side to side misalignment. The master has to be inline with the brake rod attaching point on the pedal assembly. Nearly any side to side misalignment will cause a bind. You may be able to shim between the rod and the pedal. There may be enough side to side movement in the master mounting bolts to shift the master enough to get the alignment. As a last resort, you can modify the brake pedal, but make it the last resort. Another alignment that has to be correct is the master has to be mounted squarely with the pedal as it swings. They have to move with the same angle. If one moves at an angle in one direction, and the other moves in the opposite direction, a bind happens.
If you can't figure it out, post lots of pictures of your setup and how things move. I've scratch built this stuff from a pile of parts and made the mounting brackets, so I've been through this a few times. Gene
