I have a 1995 ej1 non abs that I just re did the whole brake system. Wilwood 4 piston calipers up front, rear disk swap, ss brake lines front and back, and replaced the master. While bleeding the system everything seemed fine at first but after a few pumps the pedal would have some slack about half way then make a really loud "smash" and the pedal would get stiffer. So thinking that the system just needed to be bled all the way we continued and got all the air out of every line but the problem still continued. Brakes wont work until pedal is basically at the floor and system seems fully bled. And like I said there is slack than at about half way pedal travel there is a loud clunk and pedal gets harder

 

Did you replace the booster? It sounds like your MC is not compatible with the booster, or at least you need to adjust the push rod on the booster that pushes the piston in the MC.

 

I'd check the booster as well, although if there were a problem with the booster I don't think it would behave with what OP is experiencing.

It sounds like you still somehow have air in the system, but if you just replaced all the lines and calipers and have already double-checked everything I really can't think of where it could be getting in the system.

You're using standard DOT3/DOT4 correct?

 

You need to bench bleed the MC prior to install.

 

Did you keep fluid in the master cylinder the whole time you bled it so that no air would enter the system?
Also, it's important not to push the brake pedal to the floor during the bleed process as this can potentially damage the part by extending the plunger travel farther than it's designed to go in normal operation.