Josiah,
I'd bet on the Windshield & raise you a Cowl-vent; I've seen the water get in in both places and ultimately drip down on the shifter tower, and the rest is ... soup.
Perhaps draining, refilling with kero and a gentle run through the gears with the truck on jackstands, then an overnight drain and refill with gear lube wouldn't be extreme.
Hope there's no tragedies inside "Pandora's Box".
