Alternator and ABS Module doesn't like mud and water.
After I went though some deep mud and water on a off-road excursion and began to hear squealing noise from under the hood. Couple days after being in the mud my ABS light came on. I took to the dealer today they told me they have to put in a new Alternator and new ABS control module. It was obvious that the Jeep was sunk. (I tried to clean it up nice but there were still signs of mud) They said they will cover it under warranty but next they would not be so kind. The mechanic said I should try this time to cover the ABS module when I go off-road. Apparently water damages the ABS modules pretty easly.
Take a good look at your fan and shroud. There is a good chance you may have bent your fan. This was the reason I switched my old YJ to an electric fan. Simply switch it off for deep water crossings


