Yes, the YJ frame is a little wider. One of the reasons I decided on a large single exhaust was the fact that I would need to find room for just one muffler. I have a traction/ladder bar on the passenger side, and that would make fitting 2 mufflers a real challenge. What engine do you have in your CJ?
Gone to the dark side with an LS3 powered '57 Chevy 210