don't know if you have solved this or not.
yes you got air, I just went through this myself, and after a lot of internet searching here is what I came up with.
You said you replaced the slave on the tranny and the master meaning you have an external slave, properly bleeding an external slave on a jeep is dam near impossible. Some of us have claim to have done it and had no issues but most end up with a not so perfect bleed and have clutch issues. The actual Chrysler Bulletin on bleeding these systems is complex and convoluted and no guarantees that it will work. A quick run down of the procedure was, remove the whole system from the jeep so that you can bench bleed it, build a stopper for the slave so you don't loose the piston, hold the slave at a 30 deg angle while bleeding, press up-down-left-right-B-A-start and you might get all the air out.(or something like that) Chrysler and some after market companies offer a pre-bled system that comes complete with master, pressure hose and slave, its expensive but worth it. Napa or part source only sell the individual parts and unless you get the bleeding procedure exactly right you will most likely still have issues. My master started leaking so I replaced it, everything was good but just like you it was softer than normal, and eventually it would now work at all. it takes 20 mins to install the whole system and you're done, no bleeding and it feels like a brand new jeep.
Go see the boys at broken axle and they can hook you up with the complete system and instructions for installing it properly, all your problems will be gone.