It's way too early to be thinking about this, so my peoples that probably have a few more brain cells that aren't exhausted can help you out on this. That being said, I will give my personal experience regarding this.
I too replaced my 231 with an Atlas 4.3. I have a 1" motor mount lift, had a 2" inch body lift, and an almost flat belly pan. I took the 2 " body lift out and with the tranny tunnel being narrow on the YJ, it squeezed all my shift levers into a very small space. I did end up cutting the floor more than I wanted to, but it was the only way I could get the Atlas levers to work full range. I believe that after doing this, I read somewhere that Advance Adapters either recommends a spacer to drop the belly pan down a little or a 1" body lift to accomodate the components. I also noted that without the body lift, I get a bunch of grinding/popping from the t-case against the tunnel as well that I didn't get before removing the lift.
I think sometime this winter, I will be dropping my belly pan down a bit. Just in the last two years I was able to start parking in my garage even with 40" tires. I don't want to lose that by putting a lift back on. Sorry for the rambling, hope this made sense and helps with your thought process...