Maybe the running issue is still the exhaust, although if you got rid of a 3/4" restriction and now have 2.5" pipe out the back that should do it. Is that same exhaust tip still on there? The pics from earlier in the thread make it look like a ricer bolt on tip with a baffle plate, which will do a tremendous job of increasing backpressure, which would explain why it still feels like there's a bottleneck on the high end. It could still be the muffler itself. Otherwise maybe it's still part of the CA/Non-CA hardware that's left? I didn't read anything on whether or not you figured out if the rest of the fuel system and injectors were the same for all models, or if you stopped at replacing the wiring.
As for the aerodynamics, the roof is a rather cricial component, and it being gone, plus the parachute of the open back end and the spare isn't helping. You'll likely get better mileage with the top on if that's the cause, but nothing is going to get around the gearing/large tire issue. 4.10's and 35's is a very slow combo, even for the torquey 4.0L.
I'd say lose the sway bar and get some really good shocks on all 4 corners instead if your aim is firm handling along with controlling body roll. Sure a sway bar works, but on a ride lifted that much on 35's it's pretty silly.
Not sure if you wound up having the catalytic converter replaced as you posted, or if you just had it gutted instead, but just in case you went with the second option, if the fine and jail time isn't bad enough, you may want to think about the combination of the toxic unconverted exhaust gases and your open top/back vehicle with it's potential passengers, not to mention everyone else on the road or trail.