My only gripe with atlas is I would want a 3 speed, 1:1, something in the 2's for cruising Inbetween obstacles and not so crawling trails, and a crawl gear of 4:1 or higher. Atlas only has a 2spd and 4spd, how big a 4spd is would make it less desirable to me as well as I don't think you'd need 3 different low ranges in a manual transmission rig, would probably be worth it in an auto though.
Could always run a klune and atlas 2spd and beat on it without worry, would be rather $$$ tho unless buying used.
I'm pretty sure the TJ 241 has a yoke.