I have something to offer regarding the battery swap. Hopefully this is a good place to offer what I have learned.

Generally : When swapping my 2004 E53 battery (Interstate MegaTron to DieHard AGM) I attached a 2 amp battery charger to the terminals under the hood in the firewall. I did this to maintain voltage in the electrical system. It worked !! The windows and sunroof remained calibrated and I didn't have to re-code anything.

Also, I have a 3.0l engine, but the larger 4.4l battery (size M8/49) fit just dandy. And, the larger battery was less expensive too.