Atmel Cortex-M7(ATSAME70Q21) GPIO
1) Basically you can use every pin on the SAM as GPIO, except for some special pins like power pins (VCC, GND, ...), dedicated USB pins (HSDM, HSDP), oscillator pins (OSCx, ..), some JTAG pins (TCK, ..) and analog reference pins (AREF, ..). You will have to go through the table in chapter 5.2. Usually the pins labeled PAx,PBx,.. can be used as GPIOs

2) Chapter 32.2, point #4; Yet, they use a combined interrupt line. This means that you will have one interrupt for multiple pins and you need to find out in software which pins was actually triggered by reading the respective register in your interrupt handler

3) The EVK has additional hardware so you will not be able to access each pin directly. Yet, the board itself is pretty good and perfect for a start. By building: Do you mean a new board? You should take a look at the datasheet, chapter 58 - Schematic checklist.

4) Chapter 56.13.1.3 ff. - I/O characteristics