Just throwing something out there that may or may not be relevant, but don't count on the copper wire being good under the insulation. Twice now I've found spots where the copper wire was broken under the insulation. Usually at a spot where the harness flexes, like the bend at the firewall where the injector harness makes the bend and the fusible link bundle near the starter relay.
Jeep actually put out a TSB for this, *my TSB* after I wrote a letter and sent some pictures.
Only two ways I know to find a spot like this, one is to shake the harness and hope your ohm meter shows a fault or feel the individual wires with your fingertips to find the bad spot. The two broken ends of the wire rub together under the insulation and may or not make contact, a real pain to find.
Also don't count on those splices no matter how good they look. I've found them where somebody forgot to crimp the splice and the wires where just laying in the splice, sometimes they would make contact sometimes they wouldn't.. And I've found them where the wire was pushed too far into the splice and then crimped onto the insulation, maybe they'd make contact and maybe they wouldn't.
You mentioned the poles on the old starter relay looking cooked. Those spade connectors and the pins in the connectors get hot and loose the clamping spring type force to make a good contact. They usually turn blue or black from heat. something like that screams electrical short to ground someplace. A loose connector can act just like a resistor and change voltage and amps (watts) to heat. That is why the plastic connector housings melt melt. I always clean the connectors out and eyeball them good, a close visual inspection may turn up a problem, flashlights are your friend.
Another spot you may want to look at is the relay block, the bottom is open and packed with die electric grease, mine was packed full of mud. It looked really nasty under my relay block, green oxidation, mud and the die electric grease had turned to a tar like substance.
Pinch the wires going into the fusible links, move them around some and see what happens. the copper wire under the insulation can fatigue and break. Also look at the fusible links for discoloration, they can get iffy if they overheat, sometimes they don't blow and can act like sort of a circuit breaker and make iffy contact internally. Fuses or switches can do this also, a crack or a break in the fuse can make contact, heat up and flex (like a bi metal) and break contact cool back down and make contact again.
Just some oddball ideas, if the normal culprits aren't the problem. If your systematic search proves fruitless, you have to move on the bazaar and unusual and hope for a little luck. Been there done that.
One of the best things I ever did was pull the complete harness out of a junkyard XJ. I look at my schematic or wiring diagram and then find the wires in the harness on the garage floor, then I go find them inside the XJ.