I am dealing with a slightly similar problem with my Ranger after doing a rear Axle Swap to the explorer 8.8 (post is a few down from here).
i have gotten some information that if you have 4wheel ABS, it may have a Hydraulic Control Unit. If air gets into this, as it may have done with the master cylinder swap, your in some pretty hard luck. it can only be bled with a special tool from ford, and i have called around and the closest i found is 525 bucks. Dont as me what this tool looks like or how to use it, but they said they could do it in an hour and i refuse to bring it to a dealer.
im trying to get info on removing the HCU alltogether, and tying the three lines out from the HCU directly to the master cylinder.
this can explain the soft brakes even though it was fully bled. the unit has air in it.
mine are the same way and we adjusted the Pushrod from the master Cylinder, thinking that might be needed for the addition of the rear discs instead of the drums i usedto have, and they started locking up. readusted it back to normal and almost no brakes at all again.