For the gas...remove the panel on the right side of trunk behind battery tray...you should be able to figure out how to release gas cap directly without that cord. I haven't done it, but know you'll be able to figure it out.
On the rest...take back to body shop and ask them what they might have done that caused this. Could be, I suppose, battery is dead from not being in the car for a while...you have another key?
You might try removing switch to see if it got unplugged...but based on exterior painting, not sure why that would be.
Looks like the car came out nice...hope you like it!
Upcoming NYC dates: Jan 8 and 27. See Facebook for other shows and PM me if you can make one...love to see you there!
Mangofy your E46!