MBWorld.org Forums - Seems like a reset of some sort

Hi Guys, I am a newbie. Been visiting for about a year now. Just joined today. I got my 2009 SL63 AMG back from the dealer Thursday. Seems the dashboard has a problem and the dealer replaced it.. They had the car for 6 weeks. I have another vehicle to use and they did it way out of warranty and it was big bucks they paid for it. Mercedes USA paid for it and I am very grateful to them for this. . I don't use the car during the winter and keep a trickle charger on both batteries. So the back battery is seeming dead after the car being in pieces for weeks on end. It was most likely not fully charged when I brought it to them as I don't drive the car in the winter here in NJ. The trunk won't open or close . Roof will not open and so I buy a new battery after unsuccessfully attempting to charge it. . The old one was dated 2014. ( I may have connected a charger to the old battery in he wrong polarity.) I also saw when the floor cover was removed one of the yellow little boxes, look like a fuse or breaker, controller was dislodged from it home. This is in to the unit on the left of trunk. I believe its the power system for the trunk. When I plugged it in the trunk power worked again.
Hook up the new battery. Polarity correct, This is what I have

Warning, Reduced Brake effect, Start engine
No climate control. The indicator lights light up no fan.
I have the ABS, indicator light on
The SRS indicator Light is on
No command, it just will not start up. Dark screen. Nothing at all
The car starts runs but no brakes. The brake is hard up. Can't push. Big red warning light
The windows open and close.
The auto seat forward and memory no work

Today, I disconnected both batteries for an hour in a last ditch effort, I though I would get lucky. During that hour I put the charger on them. They were disconnected. This is where I am now. Any ideas. Seems like a reset of some sorts. I need help bad.