2007 Mustang Coupe

My mustang's battery died about a month ago and the electronics (radio, dash, etc.) were spitting out computer lingo and totally off, but went back to normal the next day. Ever since, I will start the car and the passenger window will not be fully closed, it doesn't go up into the window slot, and the line-in AUX option is no longer there. Can someone explain to me what is happening exactly?

 

Did you replace the battery, or just recharge it after it died?

A bad battery can cause all sorts of crazy things.

Did your car sit out in the rain or get wet recently? Any wetness in the passenger footwell?

 

Sounds like a case of the dreaded water leak...

Still have stock battery?
Check the user manual. It will tell you how to recalibrate your windows.

 

AUX input, I dont know.

For the Window, try putting the key into accessory mode, roll both windows down. Then hold both switches all the way up until the window is all the way to the top, hold for two seconds.
Then hold the switch all the way down untill the window is completely down, and hold for two seconds.
Should reinitialize the motors.