Its not the YJ problem of brake calipers being on the wrong side and the bleed nipples being too low to bleed all the air out of the system??? Just my .02 may stir a little thought. I have no idea what you set up looks like Marn but it is worth a look since you put a whole new axle in.
89YJ 2.5L TBI, AX-5, NP231 SYE, Ford 8.8, Yukon Grizzly, Tom Woods Shaft, 33" BFG T/As, 4" lift, Warn VR10000s.
AF Jeep Club Tail #184