The 42RLE 4-speed would be a nightmare to get installed and running in a 2002 or newer TJ and it's really not that great anyway if you have a 2003 or newer that would make it easier. Though I converted to a 3-speed auto, the XJ's AW4 4-speed transmission is a better way to go. The AW4 is a superb way to go if you want a 4-speed in any model year TJ and the conversion isn't that difficult.
Here's a writeup on one conversion to an AW4 on Stu Olson's website... there is at least one more writeup on that conversion on his website as well. AW-4 Transmission Swap - 1