When my fpp window opens "at midnight" 60 days out will I be able to schedule for the duration of my trip or just that first day that is in the 60 day window?

Your whole trip will be available once your booking window opens.

Do you know if your FPP reservations get messed up if you change your resort. For example if I decide to upgrade from POR to Boardwalk.

Changing resorts shouldn't make a difference. Upgrading to Boardwalk sounds exciting!