Most 87 MJ with auto would have had a 904 in it, not an AW4. I've got an AW4 in my YJ behind a 2.5L, doesn't really suck that much power.
Be aware that the 2.5L used a different TCU also, the shift points are higher. Using a 4.0L TCU with a 2.5L would really make it dog as the engine would never get up into it's power band. I've still got an extra 2.5L TCU if you wind up needing one. My aw4 is full manual so I don't run a tcu.