Radio code if a Becker 220. May need to reprogram the windows. Run them up and down for a few cycles. Battery will be damaged by total discharge, how much is unknown. Test voltage after a run. Get load tested before winter. Be cautious for a while.
Good that you are charging so you must know how to access the front trunk. Don't try to charge through the lighter socket and especially don't try to start connected that way.
More batteries info
here. Battery model numbers and pricing are surely out of date but the important thing to take away is a Boxster's battery is just a battery, nothing special. And good brand will do. You can swap it yourself. There are two sizes, one for the manual trans and a bigger one for the TIP trans for the MY 2001 cars. Since you are in MA, might want to get the bigger one.