After tackling the engine wiring I realized that really no wires had to be removed from the engine harness, they just "should" be removed to tidy things up a bit. The engine wiring harness was a unfounded worry. I also realized that the engine is completely independent of the jeep itself. I think some wrangler owners will try to integrate the engine pcm with their jeep stuff and that would be a headache. My biggest questions I had concerning jeep wiring was where do I get a 12v switched, a 12v constant, and which wire was the ignition. Here is what I found doing a good bit of research online, and with the jeep cj5 repair manual and a volt meter.
The first thing I did was buy a better looking engine side wiring harness. The Firewall side of the jeep has two harnesses, one that goes to the lights, and the other to the engine itself. The one I had was pretty mutilated. In hindsight though the mutilated one was just as good as my better looking one I bought off ebay. You really don't need that many wires coming from the firewall.
There are two wires you can use for the ignition switch, both are in the same plug, the wire is labeled starter. I tested this wire by putting a volt meter to it and turning the key to start, I got 12.34 volts. The thick red wire at the top of the picture is your 12v supply from the battery to the jeep. This wire supplies voltage TO the jeeps fuseblock. I ran that wire along the firewall and tapped it into my new battery cable.
The two red wires, one thick and one thin can be used as 12v switched supplies to your 12v switched feed going to your fuseblock. either will work. I chose the smaller red wire, it looks kinda orange here, but I chose the smaller one and saved the bigger one to run my 2 electric flex lite fans. It is the same gauge as my flex lite fan wires. either will work.
Because the battery sits on the opposite side from where the battery terminal is on the engine I bought a 78 inch battery cable.
I unbolted the lug holding the battery cable to alternator so I can mount the new battery cable.
I used a cutoff wheel to cut the cable that went to the battery post. DO NOT CUT THE CABLE TO THE ALTERNATOR OR STARTER. I then put a cap over the remaining stub of a cable to prevent electrecution and mounted my new battery cable. I'll add pics of the cable runs later today.
After hooking up the battery, and only the battery to the positive and negative battery cables. I tested for 12v continuity. First from battery positive to negative. Then battery positive to block, then to fame and finally body. I had 12v everywhere.
I then unplugged the positive battery cable and made my ground wire from my fuse block to the body. and ran my 12v constant wire to the fuse block, reconnected my battery cable and tested for voltage. I let the setup set for a few minutes and felt the relays and nothing was getting hot or warm.
I then unplugged the positive battery cable and repeated the wiring and testing for the 12v switched and turned the key to run. This was a hit or miss or I disconnected the battery cable rewired my ground wires at the fuse relay block with matching ga wire, positive and ground were now both 10 ga wires. I replaced my 12v switched wire due to a questionable assembly and retested. Two days later and no hickups. A good thing about building your own fuse block you'll know where the problems are if you run into anything down the road, or trail.
Finally I hooked up my ignition switch wire and ran the fuel pump supply wire. The 5.3 started no problem.