OK, to state the obvious, why would ANYONE want to swap a 3.6 in any older Jeep? IMO, that engine is really ill suited for anything actually to be used as a Jeep, JK and JL included. There just isn't any usable torque below about 1500 to 2000 rpm. I cuss my 2012 every time I wheel it. Not to mention it has made me very much more proficient on the OBDII and its near weekly exercise in extinguishing check engine codes, some of which are considerably more difficult to put out than others. In short, that engine has had a very adverse effect on my opinion of the Jeep "brand" in general, enough so that I am replacing my Grant "Jeep" horn button that sits atop my Flaming River steering column in my CJ 3B with a custom Willys Overland version. An LS or even and old school SBC is an infinitely better swap candidate if one is going to all the work involved with that.
I am really looking forward to Bronco. Hopefully Ford did a better job on their homework.