I never actual swam around to the back to check the water line relative to the hitch but I doubt it was submerged.
Regardless... I got a funny story, the wife went to get the dog's bowl from the back. I noticed the bowl and normally I'd get an earfull about how I broke the truck again so I asked if everything was ok when she got the bowl (avoiding any information that there was ever a porblem) and she had no clue what I was talking about. So I went to check it out and everythings appears to be fine.
I'll be looking into this alot more once I download a few electrical drawings, and rip open the door to see if there is a muddy water line. Just seems very strange a fuse never went and that so much was affected from this. And still strange that it all happened after I cleaned and vacuumed the interior. And now all is good... I'm baffled in a good way
Leason learnt - never clean the 4Runner or things will get fuky!
Just a tip for some who wheel... disconnect the latch on your hood so in times like this the hood can be opened from the window before you go crawling out to deal with the winch, never understood why my bddy made me do it until today.
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Limited 05 T4R -
Custom Built 6" Lift 
<--If you watch long enough he will do a backflip