Spongy pedal , low brake pedal

I may be asking a dum question, but did you bench bleed the master cylinder and adjust the push rod inside the brake booster? If not this will be the issue. ABS systems are very sensitive, so if when it fails you won’t even feel the difference. But, it will not cause the brake pedal to suffer the way you describe it. Don’t forget to do a bleed in the whole system even after you had bleed the master cylinder.