I've heard of this one before on another post... It's one of those "my computer doesn't turn on... did you check the plug?"
Well make sure that the right side caliper in on the right side, and the left is on the left. It sounds stupid, but the bleeders are specific, and make sure air isn't sitting in a pocket.
I have a 95 YJ with a D30 & F9" rear... I haven't had good brakes in years... It's almost scary at times. I've bled them too... I had brakes, life was good then I took a rear caliper off, compressed the brakes (by accident) and haven't had a good pedal feel ever since.
I wish you luck, and I hope that someone here can help!