i used to carry a big jug of water with me and after each dirty water crossing, i would shut the truck off, douse the alty with clean water and then spray it with WD40 to force the last little drops out. nismojunky taught me another trick - rev the shiat out of the engine after going through the water hole and it clears a lot of the grime out. Best to carry a trail spare with you and keep an eye on your volt meter. Clear water doesn't hurt them very much, it's the chocolate milk and packing it with mud that ruins them.
if you cant afford a skid plate, at least go to the JY and get a factory splash guard. Something is better than nothing.