Where would the jeep spend most of its life in?
For off roading I would keep the efi. EFI will work perfectly no matter what angle or elevation your jeep is in but I would change it to TPI instead of TBI with vortec heads as mentioned above. Also as mentioned above you would be better off with 4.56 or 4.88 gears but that's only if most of the time you would be off road. For highway, leave it as is or change to a carb with the 4.10's. Either way with the lift and tires you have mpg's will suffer.
Any vehicle built for too many different applications will not be perfect at any of them so try to build it for the application where the vehicle will spend most of its life in.