Not surprised about the warranty, but it seems the following components have failed or are failing - alternator, rear axle, locker activating randomly, third brakelight. I have been in mud on many occasions (never so deep that I got stuck though) and have not had any adverse effects that I know of. Some of his issues seem to be shorted electronics.
I have not worked on trucks other than Toyota but the connectors on Toyotas are well done compared to what I see on other car brands. Wires potted where they enter the connector and an internal o-ring.
My ADD detection connector failed (4WD light would not come on even though I was in 4WD) but it was because it was continuously being bathed in oil from the valve cover leak.
Also I wonder if it's better to have conventional brake light bulbs vs LED. I believe the LED units have small circuit boards associated with them and perhaps it's difficult to prevent moisture damage on these?