Painful Wiring would be expensive. Besides, he's gotta have the computer flashed also.
I have a Jeep CJ body on a YJ frame with the 5.3 Vortec which is a Gen III like yours. Though the cubes are different, the install is the same. So here goes:
Contact Jesse Bubb through this website for your harness modification and reprogramming your computer. He has done 6 harnesses and ECM's for me and my buddies and all have worked flawlessly.
Wait4Me Performance Tell him your requirements for smog legal and that you will be running the 4L60e. He can also performance tune the computer. You will need him to turn of the VATS (vehicle anti-theft system), but he'll know that if you tell him it's going in a Jeep. The harness and computer will come back to you with about 5 or 6 wires to hook up and that is all. It will probably be in the nieghborhood of $400 for programming and harness modification.
Now for some install notes from my build:
It may be a tight fit for your exhaust manifolds between the firewall and frame. I have a 1.5" body lift so it wasn't an issue. Just telling you this so you know that it can be done with the factory manifolds.
Your oil pan holds 6 quarts and hangs down pretty dang low. If this is a concern to you after the install, then you can purchase an Camaro LS1 pan, gasket, pump suction tube, dipstick and tube from GM for about $250. It is a 5 quart pan but is 3.75 inches shallower (level with the transmission pan).
Next is a fitment issue you need to look at when mounting the engine. The 6.0 has a taller intake than the rest of the Gen III's. Check your hood clearance before setting the mounts. It should work because I have seen them in CJ's before. I believe any other Gen III intake would work, but will not have as much torque.
Next is cooling. I'm running a 3 row CJ radiator that was for any V8 CJ. I have my transmission plumbed through the radiator with no cooling issues. You will have to get creative with the radiator hoses and heater hoses unless you buy an aftermarket radiator made for this swap. PM me later if you want more details about the plumbing. You will have to ditch the mechanical fan. The electric fan I used is from a Ford Focus and fits perfectly. It keeps the engine at 190 in the summer.
The gauge hookups all depend on what type you plan to use. I use an electric temp gauge and was able to find a $10 Autometer adapter and sending unit that utilizes the allen head plugged port on the passenger side head. The sending unit for the ECM is in the same port on the driver head and must remain there. I use a mechanical oil pressure gauge and was able to tap the oval shaped housing down by the oil filter with an NPT tap to install the tubing.
Are you going to make the motor and transmission mounts or purchase them from Advance Adapter?
