I took an 88 Wagoneer 360 and put it in my 88 YJ. I love the 360! Great torque, runs like a top, easy as hell to work on! I went with an HEI ignition to simplify wiring and it starts practically instantly. I still have the stock Motorcraft 2bbl on it but it runs great so Im not fooling wtih it. I think a 360 in your CJ is a great idea. I think you will be pleased with the result.
88 YJ...kinda. Clayton Hard Arms, V8, 1 tons running gear, twin sticked, Irok's, fuel cell, multi-colored