I recently had to replace my alternator as it got "water damage." according to the dealer. I couldn't find an aftermarket one so I ended up spending 698 for a new factory one....
One thing I noticed is if you look above the tire on the passanger side, you can see the alternator and it's completely open to the elements....instead of at least being higher up on top of the engine.
The muddy water I went through came up to the doors on my stock truck and I was told I should replace all my fluids also???
I also have an issue after washing under my truck with a pressure washer, the throw out bearing makes noise. It's going to cost me 400 to replace the bearing, but a friend said if it feels normal it should be ok for a little while???