CJs are narrower, have leaf sprung front axles, and (like you already said) have the pumpkin on the wrong side. Forget a straight bolt in, i dont even think it could be made to work, even with extensive cutting and welding.
I dont own a CJ, but i have been around them a good bit. I do own an MJ and have done extensive work on her.
the stock D30 front end is pretty capable and can handle 33s fairly well. And even though we all know the rear D35 is crap, it can handle some stress. If you to get rid of it for something better, look for either a ford 8.8, chr 8.25, or (SUPER rare) a comanche D44. There are others, but these are the most commonly known and swapped.
231 T-case is a pretty bullet proof as well for light offroading.