Swapping rear TJ disc brakes to rear TJ Dana 44

Then you will need the backing plate from TJ rubicon, or other TJ with rear Disk, or LJ (all LJs had disk).
 
This backing plate will simply fit to the axle, as axle ends are identical regardless of whether it is a disk or drum
 
You will also need new ebrake cables, I bought 2 from AutoZone. Any Ebrake cables for TJ with Disks will fit, but LJ ones will be too long, so dont get the LJ ones.
 
I used the old calipers as a core for new calipers from autozone, new rotors (all TJs seem to use same disk rotors), brake shoes and pads.
 
You will need to use different brake lines on the axle itself, as calipers have new flexible part that drums didn’t have
 
You will need to drill a tiny hole on the spring perch to screw the brake line to it. It is an important step, don’t miss it
 
As for the master cylinder of combination valve changes, I did not change anything. My understanding is that these parts are same for all TJ and LJs of 2003 to 2006, as in these years it came with Disk and Drum. Also, it drives and stops fine. Not ideal, but i dont thing that even from the factory it was as good