I recently put a yj tub on my cj. The only issues you will have are some of the body mounts. For example, the mounts in front of the rear tires will not line up with the tub. I don't plan on using them cause I am going to tie my cage into the frame in at least 6 places. They will act as body mounts.
Also the rear frame mounts on the crossmember will not line up exactly. You will have to open the holes some.
All in all its an easy swap.
Some other things you'll need to keep in mind is the cj defroster duct. The cowl on the body is different. You'll need to come up with some ideas for that..