Top won't close and front windows won't roll up
 

I parked my 09 cooper s in the garage last night with the top down. It has a bad battery so I jump started it this morning. When I did, I got the error light with the mini on a lift ( vehicle electronics have failed). My top will not close. I hear a click in the relay but that's it. My front windows will not go up also. I push up on both window buttons but nothing happens. I pushed up on the button to roll up/down all windows and only the rear ones work. I checked all of the fuses and they all seem good. I am very confused. Did mess something up when I jump started it? Please help! Thank you!!