What year YJ? Is it carburated? What tranny, flywheel and bell housing? If your gonna try and keep the fuel injection, alll is a four letter word. It really isn't that complicated, but there are a whole bunch of wires. Pretty much everything except the front light wiring, which is bundled with some of the motor harness. The three front harnesses (with the components, ignition module, relays and such), a good wiring diagram, a box of colored pencils and a lot of patience. If you have a printer that can blow up the diagrams, it will make it easier.
There are guys that have been trying to figure out the whole system for 17 or 18 years and still get surprised on occasion. Some of the wiring, is spliced under the wrapping and in some places wire color changes at a connector (though this more common in the rear vehicle harness).
Don't forget the gas tank also, your gonna need the fuel pump.
I´m probably gonna do the same, when I find a good YJ body with a blown motor. I´m also gonna stick an AW4 (and wiring) in there, which will make hooking up the crank position sensor a whole lot easier.