Did you replace the master cylinder? If not you can get the same symptoms with a bad master cylinder. Mine did this but the soft pedal was intermittent and slowly got worse to the point it would barely disengage at all. Fortunately, it was still under warranty. The first replacement was also defective and they had to install another. No problems since then.
One thing I did when the master cylinder was bad to get it to work better was to push in the clutch with the engine off and side step the clutch pedal to let it slam up. I don't know if that was a good thing to do but it worked better for a while.
2002 FX4 Bright Red Supercab 4.0 SOHC, manual 5-spd & Tcase, 33" BFG MTs, K&N air filter, Modified air box inlet, Gibson SS cat. back exhaust, Bama flash, Hidden Hitch round receiver, Rear helper air springs, Electric trailer brake controller, Line-X bed liner, WAAG bar with KC lights and Wildernest shell.