(a) make sure the brake bleeders are at the tops on both rears since you just installed it, might have accidentally swapped the calipers.
(b) the brake bleed procedure on the MJ, with stock braking system (did you eliminate the rear height sensing valve?) is special! You bleed all 4 in the normal order, then open a front bleeder and slam on the brakes to shuttle the bypass valve in the proportioning block, then bleed both rears again (right, then left) with the front still open, then bleed all four again normally. This is because the MJ braking system has two lines to the rear brakes, one is a bypass line and the other is used normally. If you don't get all the air out of that line by enabling the bypass temporarily you can/will have a soft pedal.
Try bleeding the master cylinder with it held so that the fittings on the side point up at about a 45 degree angle, I find this helps persuade the air bubbles to move into the lines faster than normal. Also, you might look into a WJ or 95/96 XJ booster+MC - they will increase your braking ability greatly.