Main Menu: A
Modals: Yes please. Though personally, I don't think that goes far enough. NavigationController drill down menus is what I expect on mobile. If the page has sections, you need a submenu.
Saving: Save immediately (unless it's an option that affects large groups of users, my access or anything else that could possibly be dangerous).
MobileOptions and Preferences: I think the proposed distinction makes sense. I personally summarise these as "Minerva settings" and for me logically, they belong under "Appearance" under "skin preferences". But I understand highlighting them separately in the Mobile interface.