If I remember correctly, California (as per you location listed) has laws governing the swaps of vehicle engines.
First, the engine swapping in must be of the same year or newer
Second, if vehicle came equipped with Fuel Injection, then the new engine must also have fuel injection.
Third, the emissions testing people will check that the swapped in engine produces less emissions than the original stock engine was designed to emit.
If you can pass all those tests with either engine, then
Now, as far as the work involved, its all the same amount of work. Its better to get the engine, transmission and transfer case all as one piece. The stock Jeep axles will be strong enough to handle either engine, and you will have the added bonus of the 4.10 gears! Fit either 33" or 35" tires to those axles and have fun.
If I remember the FAQ properly, the rear axle might have problems with 35" tires unless you do the Super35 kit, but till it breaks, I wouldn't worry too much about it.