It's not that much of a pain the butt...
I got a yj ax15 and it did have the different clocking but better up than down especially for wheeling....
Here's mine...I just banged the tunnel a bit to fit the transfer case but it fits...,just make sure you have the ax15 crossmember with the 1" drop it helps a lot....
Got about an 1/2 clearance between the case and the tunnel