I swapped a ford axle into my yj. The diff pinion is about 1" (quite possible more) off alignment with the tcase output. No problems whatsoever. But it also helps to have a driveshaft as long as possible b/c it makes the ujoint angle less. My driveline is about 20".
-Dorian
88 YJ w/ factory paint
-Dorian
88 YJ w/ factory paint