I have never done it but not sure why you believe it must be a manual. A quick google search shows plenty of people doing it. With the correct procedure it appears to be ok. See the link attached. Transfer case in neutral and gear select in park with the key in one click forward position.
http://www.rvforum.net/SMF_forum/index.php?topic=21482.
I'm sure there will be plenty of opinions on here on this one. Jeep lost forum also had some info on this.
As for the KJ itself, there are a few things to look out for dependant on if you choose diesel or petrol but on the whole I would think the petrol would be the safer choice with less chance of issues. There seems to be a steady flow of questions regarding issues with the diesel but few with the petrol. Again, if you can find a good clean diesel with great service history then go for it but any diesel without a good service history would be questionable. I've got an 05 petrol and never had any dramas engine wise. If your chasing fuel economy and any sort of mileage then diesel is your choice hands down. The petrol is thirsty! The usual kj issues after mileage are the window mechs fail due to a crappy plastic bit. Easily repaired with a steiger replacement. Suspension components, Bushes etc will require attention on higher mileage cars and the aircon will most likely not be cold on most models unless it has been repaired. Cv's and unis will require attention but that said after 80k I've only just had to do my first cv on the transfer case end of the front propshaft. I'd say they are all pretty minor and no real show stoppers. Go for it! A comfortable ride and quite capable off road. The front diffs are not strong for abuse but I'm guessing you don't plan on rock climbing. As a tourer you'll have no problem.
Plenty of good advice and aftermarket stuff available for them if you know where to look and i'd say you have already found the key to it right here on AJOR.
Good luck.