Again from Novak, the NV3550, as found in TJ Wranglers from 2000 - 2004, as well as the AX-15 found in earlier TJs, adapts to the Ford "butterfly" bellhousing through an adapter kit:
http://www.novak-adapt.com/catalog/kit_fm3550.htm
I'm pretty sure that includes the 4L 6 cylinder, but I'm not sure. This solves adapting problems, at least - provided the wiring loom from the Ford engine is used, it
should be "plug-n-play", so to speak.