2004 F-150 4x4 help

In late February of 2004 i purchased a 2004 f150 stx short wheelbase 4x4. It has 4.6 liter v-8 and an automatic transmission. I have put 14,000 miles on the vehicle to date it is currently settin in the service department of my dealship with the transmission out of it. Since purchasing the vehicle i have encountered many serious problems. The front pinion seal of the rearend went out and the rearend was making a loud whining sound. The dealerships said the pitch of the rear end was off. I have been around vehicle all my life and worked on them too and I have never heard anything about the pitch of a rearend. The vehicle also puffs black smoke and sputters on cold starts and take off it has been to the dealership 3 times concernin this and still no solution. It also aquired a large crack in the windshield after settin under the carport for 2 days the dealership said it was a stress related crack. Currently the transmission is out of the truck overdrive was completely out and drive was slippin to bad to drive it. I receive a call saying that the transmission, front differential, and transfer case on the truck were full of water and that my warranty would not cover replacement of the part because of exposure to water. The truck has never been off road the only water exposed to was water standing in the road after a rainy week around in my area and that water was not over 8 inches deep. How does water get into a vehicle like that and should ford cover repairs and what in the world is rearend pitch. Plz Help me!!!!!!!!!