The above may very well be the problem.... the existing MC does not push out enough fluid to activate disc calipers at BOTH ends. It runs out of stroke before enough fluid can be pushed out. The fact that the front work fine with the rear line pinched would be another indicator of that.
Here is another thread just updated to indicate this was the solution on a 4 disc setup:
Wilwood/Strange 4 Piston Calipers soft feeling pedal
One thing that is important is to make sure the the pedal and rod and MC setup is such that the MC pistons are coming as far back out in the bore when released as possible to give maximum stroke.
