Stereo and Auxiliary Audio input problems after jump starting.
 

Hello
I jump started my 2007 Ford Expedition Limited per the owners manual instructions and immediately following noticed the following problems:

1. the AUX button no longer showed LINE INPUT as an option. It only shows SAT 1, SAT 2, SAT 3, and RSC ? (whatever that is).
2. the Volume, Media, and Preset Radio Station button on the steering wheel also no longer respond
3. the CD player gives me the CD ERROR message. When I press CD, it will say INITIALIZING for a few seconds, but does not work. Also, I have at least one disk in the 6CD changer that will not eject or play. When I start the car, the disk changer makes noises like it is trying to load or change disks, but nothing happens.

I have checked all the fuses at the Power Distribution Center and Fuse box. (Right front passenger and under the hood), but they all show to be good. I have also disconnected the positive terminal on the battery for 5 minutes and reconnected, but again no changes. Can anyone think of a solution, PLEASE?
BTW: I still have an extended full warranty through Ford. This should be covered, right?