Craig, thanks for the compliments! The links I provided cover a lot of ground with the troubleshooting and understanding the functions and identities of the various Jeep 2.5L TBI components. Our forum exchange was a hands-on like yours, and some wading through the materials should provide insights. Of course, I'm pleased to go further if you exhaust the details offered and haven't solved the problem!
You mention the wiring harness splicing and butt connections, and that is a concern. For EFI sensors, the important signals for the ECU are dependent upon wires with integrity and the correct resistance. Butt crimp connectors are terrible when resistance is critical: There is no assurance that all strands of the wires will make contact. There's also the risk of moisture wicking into the connector and up the wire insulation, a problem that worsens with humid climates, 4x4 water fording and even the occasional clean up at the car wash! Crimp connectors work for trailer light wiring and other tasks where resistance loads are not critical—just step up wire gauge and use the right fuses!
Also, you described the sensors looking like mud and acid. Shorts to ground or voltage leaks to ground can result. Like a dirty battery case, if the sensors are encrusted with conductive material, and that can include soil with minerals, there could be voltage leaks to ground. The terminal of a sensor could be shorting mildly to the brass or metal shell of the device and creating resistance or voltage changes. Even minute voltage changes can throw off a sensor signal to the ECU.
If you cannot find harnesses or a harness change-out appears daunting, you can repair wiring properly and get good results. I like to use rosin core solder and seal the solder joints with multiple layers of heat shrink tubing.
First, I place fresh heat shrink tubing, cut to the right lengths, well up the cut wires and away from the soldering heat. Take the stripped, opposing wire ends and interlace the bare wire strands together—facing toward each other. Minimize the diameter of the bare wire joint; mimic the diameter of the insulation if possible.
Now you can solder the braided strands together, using rosin core (not acid core) solder. Add rosin paste as desired to assure solder flow through the bare wire strands. A finished solder joint around 5/8" in width works well, using a smaller soldering iron or a soldering gun.
After the solder joint cools, slide the heat shrink tubing over the bare soldered joint and insulate the section. Shrink the tubing carefully to the wire insulation without melting the insulation. The tighter the tubing against the insulation, the better seal. You can double up with a couple of heat shrink layers...Done correctly, heat shrink can prevent shorts and moisture wicking.
Note: To shrink tubing, I use a heat shrink gun, heat gun or even wooden kitchen matches with the flame passed quickly around the tubing without melting the wire insulation or burning a hole through the tubing. Practice on an old scrap of wire.
Soldering takes time but can save wiring and make permanent repairs. Unless the current damage is extreme, avoid replacing harnesses. I like your approach: Restore known wiring issues first. Later, the troubleshooting will be accurate and reliable—like you want your Jeep Wrangler to be!
Keep us posted and share interesting developments. Troubleshooting will be straightforward once the wiring is in good shape.