Not sure about the auto used in a TJ, but the AW4 auto in an XJ has a shorter input shaft than a TJ 5speed. So when I was putting the TJ Np231 into my XJ, I had to swap input shafts or cut the shaft. I took the hard way and swapped shafts. If I was going the going into a 5spd TJ, it would've slid right in with no mods.
