You can use an external EEPROM if you want to load the firmware for the FX2LP on every boot from the EEPROM.
Please refer to FX2LP boot options.
GPIF mode uses 8 bit or 16 bit data transfers on FD bus.
Yes the pins PA4, PA5, PA6, and PA7 can be used a GPIO as they are not configured in GPIF mode. Please refer to section "15.5.2 IFCONFIG" in IFCFG[1:0] table from the EZ-USB Technical Reference Manual .
Thanks for the information!