I personally think the 4.7 and 46RHE is not a good choice for a buggy. I wheeled with that combo for 2 years. The tranny never broke on me, but I have been told by the new owner that he has had some issues with it. For a while I was planning on building a WJ buggy and I spoke with several individuals who have transplanted the WJ's drivetrain into buggies/jeeps. All of them said it wasn't worth it. The wiring and computer is a nightmare. The tranny is considered weak and it's not really upgradeable. The tranny parts are $$$'s.
If you want some info call Dan at Burnville Offroad. He put one in a TJ. You can also call the Curries. They have done two swaps...one for the 'fire ant' and one for a customer's TJ that is on 40" MTRs.
IMHO I would just stick with something common that is easy/cheap to mod/diagnos/fix.
Just my $.02
Mike