2011 Mini Cooper Questions

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Bf jumped the car after the battey died. Now the windows are unresponsive, the interior lights (colored,roof) dont work, and the blinkers dont work outside nor in. Everything else seems to be fine. What could this be. Tried the unplugging and letting it sit of the battery. Nothing. Tried banging on the panels in the doors. Nothing. Tried toggling the switch for the windows. Nothing. Checked all fuses. They are all fine. Not sure where to go know. Im thinking its becaused it was jumped but how can i fix it and how much will it cost or is there something i can do. Pretty handy myself.
Yellow check engine light. Tried erasing with code reader could not remove.
I had water leak in around the sunroof of my MINI and when it found the lowest point it exited to the right of my glove box. Shortly thereafter, Windows didn't go up or down, headlights come on when engine starts, turn signals don't actuate, dash lights stayed on after key was removed, Key gets stuck and will not come out After engine is off(push button start).
I'm being referred to a MINI dealership - what am I looking at here in time and parts and MOOOOOLAH??
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