wilwood problems

Without regard to what goes where, if you cap the mc at the frontmost port, leaving the rear port operational;
Then the frontmost chamber is hydraulically locked (assuming it is air-free), and so whatever is connected to the rear port should show a hard pedal.
If it does not; Then either there is a mechanical problem in that system, or a hydraulic problem.......... or there is air in the frontmost chamber acting like a spring.

Therefore
1) I recommend always to rebench-bleed the mc looking for the telltale bubbles escaping from the compensating ports. During bench-bleeding, sometimes you have to introduce one-way valves so the fluid doesn't just shuttle back and forth; I use my fingertips. You may have to bench bleed with one end higher than the other.If you cap all the ports the pedal should get rockhard as the only flex will be in the firewall. After re-connection, if the pedal is still soft;
2) I recommend to C-clamp the pistons into their calipers , all of them and pedal test. If still soft, obviously you have a hydraulic issue. And if now hard, just as obviously , you have a mechanical issue.