Frank,
There are so many reasons why it's hard to tell without seeing the vehicle.
Who replaced the master cylinder? They should be bench bled before mounting on the fire wall.
If your pedal is low, you still may have a caliper or rear wheel brake cylinder leaking. You need to go underneath and check for sights of wet/damp fluid around the brakes.
You may have to pull the wheels and drums off the rear to see if there is any seepage around the wheel cylinders. Remember the outter rubber cover on the wheel cylinders is just a dust boot and so you sometimes have to peal the boot back to see if fluid is leaking past the seal, but has not leaked out from the boot.
In any case, if the pedal goes to the floor, you have a hydraulic leak or the master cylinder is defective.
The only other possiblitiy is a defective brake booster or ABS system, but if it was the ABS you should have gotten an ABS warning light.
If you don't find any leaks, my first step would be to completely flush the brake fluid at all 4 wheels and replace it with fresh fluid. Especially if this had not been done in the past 3-4r years. Brake fluid is Hydroscopic and will attract and hold moisture from the air. Water is heavier than brake fluid and will migrate and settle in the lowest part of the brake system, which is the calipers and brake cylinders.
The heat from the brakes turns the moisture to steam and when you press the brake pedal you are just compressing the steam (gas) and not getting your full braking action.
I have cured a lot of weird brake problems just by flushing out the old fluid and replacing it with new fluid.
....Rich