is there anything I need to know before disconnecting the battery? Should the key be in or out of the ignition? Is there anything special that needs to be done to restore settings, codes, etc?

No, just disconnect, R.O.W cars have a battery backup for alarm and I'm sure you guys don't, If you want to be safe just leave the key in ignition turn once until all lights light up then disconnect the neg on the battery first.

You might find when the car starts up that it's idle is a bit over the place, this is normal. Just trying to find it's settings.