If the engine runs well, find out from the state emissions tech center (NOT a testing center, although they could tell you who to call)what it needs to be legal before swapping motors.
In Colorado that rig could have a 50 state legal Howell TBI system installed on it and a new cat and you are good to go. Way easier than a motor swap and will run better.

As to axle gears those can be changed to match whatever size tires you want to run.

Nobody said building a jeep is cheap.

SD