I ran the cj setup with offroad X pipe and stock axle backs. Honestly, you will not see the gains up top (whole point of the cj) without at least a offroad midpipe IMO. I know people say you don't gain anything with axle backs, but I did notice going to a straight through 3 inch race muffler the car feels stronger 6800 up to 7600 range.
If your not going to run offroad pipes then I would recommend doing first some Kooks headers and high flow cats with a more straight through (non chambered muffler). Or offroad midpipe with straight through axle back with stock headers. Either setup would be pretty equal power wise assuming similiar gas and tuning. Aftermarket headers and offroad mids would give you another 5-12hp at peak.