if you're talking about putting the wrangler stuff into the MJ, yes, the wrangler t-case will be clocked up a bit, but no you won't have to redrill if you don't want to. I've got a wrangler AX15/231 in mine and it cleared barely but it cleared and now I get the benefit of extra ground clearance. a few guys needed to hit the floorboards with a big hammer, but even then it's nothing crazy.
you will want to source yourself an XJ/MJ AX-15 crossmember and shifter plus shifter tower. I've got the TJ shifter in mine and it's doable, but the bends put it right up at the dash in 1st/3rd.