I was unaware of that Bobby, thanks for laying down the klnowledge.
Do you know what master you are running.
This is what I am thinking, When I swapped to the D44's, my stock YJ master couldn't stop worth a dick. I went with a 1986 E350 Master, very little modifications to get it to bolt in (little bit of grinding on te emounting ears to clear the booster) and it would stop better than stock once I got a master that could supply enough volumn for the larger calipers.
Another option is to pull the master off and check length of engagement on the plunger as it enters the master. should be adjustable on the end with a set screw. but I am more or less thinking that the stock CJ master simply will not supply the volumn needed for those calipers. Also if you add disc rears, I found that a 2psi residual pressure valve really helped with maintaining a good pedal at all times.