As for the possible electrical demons form muddy water...
Muddy water can contain all matter of chemicals, salts, organic compounds, and other nastiness. It also conducts electricity to some extent. Between the two:
- Stray voltages and rapid temperature changes can damage semi-conductors and shorten their life. When a random transistor dies in a chip, the output can become erratic under completely random circumstances (i.e. between 83 and 86 degrees ambient air temp and only when capacitor C2 is charging). Those are always fun, and sometimes expensive, to track down.
- Impurities in the water can be left behind in nearly any connector (plug or bolt-to-frame), switches, crevice, and even in the ends of the wire itself. Because the macro-impurities washed away does not mean the micro-impurities that you cannot see did. The impurities give a hold to future moisture to collect and cause all manner of fun mainly due to increased corrosion. The only way you're getting away from that is alcohol/WD40 scrubbing every possible exposed connector individually and then coating with dielectric grease before assembly.
- As previously mentioned, stray voltages can cause wire overloads that oxidize or otherwise damage wire in unseen areas. Particularly at risk are smaller digital-run wires and grounding wires. Leads to really dirty signals that computers have a hard time decoding. Goes back to the fun debugging.
Not to say any of this happened, is a given, or even likely depending on what exactly was in the water, but it's all possible and the chances increase the longer the truck spends in the water. Just because you went through all of the connectors and they looked clean, dry, and non-corroded don't completely discount what the guys are saying about the increased possibility of future electrical gremlins. Sounds like you're about to replace most of the drivetrain harness so it should alleviate most potential problems, but the rest of the electrical (infotainment, comfort controls, locks, etc) was still exposed. Just something to keep in mind in the future if things start acting up.