MK5 GTI Will not start

[Mattlock]

Also I can't simultaneously open or close all the windows - just the passenger side ones work, and the others stop. No idea if that's relevant, but strange none the less.

That's probably related to you swapping the battery. When there's been a battery disconnect, you have to reset the auto window closers by winding each window (one at at time) all the way down and all the way back up and remain holding the up button for about 3 seconds after the window has closed. Then they will all auto wind up and down from the key as well as the driver's door control.