Brakes Foxbody Brakes still soft

Assuming the car is a 1986 by your user name. Does it have stock spec brakes, original soft lines, and the original booster? What rotors and pads are on it? Still drum brakes in the rear? Did you convert it to a full SN95 setup? If you set the e-brakes will they stall the car if it’s a stick or hold the car with it in gear for an auto?

Lots of details you can provide that will help to figure this out.
 
More information: The Mustang is an automatic with the 5.0. The car features new drum brakes in the rear, while the new master cylinder is of the same design as the original model. The front brakes are stock (not including brake pads). original brake booster and brake lines. The E brake does seem weak. The pedal is very stiff when turned off. but almost to the floor when on.
 
Does it pump up when the engine is running? In other words do a quick double pump on the pedal and see if that firms it up.

Engine off. After a few pumps to bleed off vacuum, is the pedal rock hard with little to no travel when you stand on it?

The combo valve unit is notioius for rusting up and causing bleeding issues. When you bleed the brakes, do you get strong flow from all the bleeders, or does one or more brakes dribble out?
 
It doesn't pump up when running
Does it pump up when the engine is running? In other words do a quick double pump on the pedal and see if that firms it up.

Engine off. After a few pumps to bleed off vacuum, is the pedal rock hard with little to no travel when you stand on it?

The combo valve unit is notioius for rusting up and causing bleeding issues. When you bleed the brakes, do you get strong flow from all the bleeders, or does one or more brakes dribble out?
No it doesn’t pump up when running. And when it’s off the pedal moves an inch and half but it doesn't pump up either. And I don’t recall having any flow problems when bleeding the brakes.
 
Its either a bad master cylinder (yes you can get one new out of the box) or it was improperly bench bled (sounds like you know how to to do this) and/or you need to inspect the soft lines on the front calipers and the one above the pinion of the rear end for swelling when the pedal is pushed.
 
The symptoms you describe tell me that the master cylinder needs a bench bleed or is defective, air somewhere in the system.
40+ year old car needs a good brake system inspection and rubber line replacement..
 
How did you bench bleed the master? Air in your lines is the most likely. Sometimes bench bleeding the master gets people. Running down how you bled the brakes would rule that out.

Rear drum brakes not adjusted properly can cause a spongy pedal as well as a weak e-brake. Are the shoes adjusted close to the drum? Slight resistance while turning drum.