It wasn't technically hard but there was a lot of work to it which took the better part of a weekend... and oddly enough everything worked fine after a friend & I were done. But that was on my previous '97 TJ and there'd be a little more to doing that kind of swap to your '06 where the 42RLE transmission used for that is computer controlled where my '97's was not. I paid roughly $1100 for everything once I was done but I did get a smoking deal on a complete 32RH package which is the automatic transmission used on 2002 and older TJs with the 4.0L engine.Was it hard to convert it to an auto? Was it expensive? What year did you take the Auto from? Manual is fun an all, but since I drive downtown daily it gets annoying sometimes
There's another better transmission you could convert to called the AW-4 (also a 4-speed but with a much better Overdrive ratio than the 42RLE) which came in older Cherokees but I don't have a clue on if that is easier or harder once you get up to newer TJs like yours.