I missed the mention of the 5.0 in my original post. Ignore that one.
Not a common swap. Trying to make the PATS and ECU work with anything other than the stock auto would be a pain in the butt. Would it bolt up? Sure. Would the transfer case? Doubtful. The Mustang was never made with 4 wheel drive (obviously) so there would be transfer case and driveshaft issues. You'll definately be in for a challenge trying to find someplace that can hybridize the trans to accommodate a transfer case.
I'd be looking at a manual trans out of a pre-97 F-150. You could use that one, bolt a manual transfer case to it (or even an Atlas case) and still have the 4wd. It may still require some fancy electronics to make the engine run, but might work.
-Joe