Craig, Go here and read every page.
DazeCars, Mustang IRS or Independent Rear Suspension page II
Page 4 has some interesting info re Dana 44 parts and Jag Diffs. ( some well kept secrets)
The site will give you a good idea in what's involved in stripping and reconditioning the Jag diff.
Also good info on shortening the drive shafts and LCA.
And after you've read all that you can go here and see what other people are doing with the Jag diffs.
http://irsforum.boardhost.com/viewtopic.php?id=242
EDIT: As to a possible repair shop to change the ratios, I know years ago diff lapping at Kedron was the place to go but I'm told the old guy who did the Jag stuff is no longer there. Also they seem to have a set starting price for Jag diff repairs. $1000.00 is the minimum I'm told.