[GORILLA]

hi, i can't imagine how at every rain, the fuel get's water in it.
assuming the hood is on, that discounts under the hood. after it rain's i have opened my hood & it's dry, even here in florida when it storm's, with wind gust's blowing the rain sideway's. even in down pour's.

so that leave's the fuel tank, and the fuel filler, & the cap.
since the tank is under the truck, with a shield covering it, i can't see that happening, unless it has a hole in it.
the filler tube could be it, rain does get into the fuel filler cover, it run's down the side of the truck & into where the cap is, BUT there is a drain hole.

now the fuel cap, unless it isn't tight it might allow the rain in, but if you were to take the cap off start the truck, it will through a code. so that can't be it.

maybe you are looking at the wrong thing's like mostsleek said.
anyway, i hope 1 of our toyota service tech's here (ASE mechanic's) can shed some light on it for you.
good luck,
gorilla