I'm in the process of putting that motor into my CJ 7. I am using a 727 auto with the amc tailshaft for the shortest length. I am using a 231 tc with a slip yoke eliminator, but I am drivers drop with my front axle.
I think to make the 360 work in a cj5 you would have to use a manual trans. unless you are stretching the wheel base. But that is just a guess... you can make anything work with some time!