Brake Fade Issues

Hi all, this is a pretty basic question, I think. My Scamp recently started braking really badly (fading, pulling hard to the right). I found that the front wheel cylinders were both bad. One leaking, the other stuck. I replaced the cylinders, drums, wheel brake lines, and bled them. They now work fine with light braking, but after extended use or even one hard brake, I now experience massive brake fade. The pedal goes all the way to the floor and I can even sometimes completely depress it even if the car seems to be otherwise braking fine.

Looking in the master cylinder, the brake fluid appears very dark brown, even after putting in at least a pint of fresh fluid, with what appears to be a sort of sediment. It looks like the inside of the master cylinder is rusty, and contaminating the brake fluid. I suppose this might be what caused the wheel cylinders to go bad in the first place. I know that brake fluid is hydroscopic, but would this cause the brake fading issues?

To fix this problem, can I just flush the fluid, or do I need to remove the master cylinder and clean out the rust first? Can I attempt to clean it without removing it from the car? I'm just afraid that if I remove it I might cause more issues.

First time working on brakes here... Thanks for the help!