...But correct me if I am wrong did they not drop this transmission in the stang?...
...I miss the live axles...would makw this easoer to find a solution for lol. The company I work for made the open diffs for the ls.
Search through the board there is a guy who did a lot of work on mangling up some CV axles for the rear in order to get high HP/TQ through them. He ended up giving up on the stock knuckles and is fabbing up arms to mount C6 vette knuckles in the back. He put an 8.8" center in it (easy mod) and is using F150 4x4 31-spilne Inner CV joints and re-splining one end of the C6 vette intermediate shaft so that it will fit to the Ford inner joint. He ended up somewhere around $800 in parts for this set-up versus $2200 in a custom CV axle. That of course doesn't include his time/labor.
The LS uses the same automatic transmission as the mustang just with a different bell housing pattern and torque converter on it. Everything from the pump to the output shaft is the same.