The following pins are not used in the software packages:

Pin Pin number Direction Type
AVR_RXD AW35 IN LVCMOS25
AVR_TXD AY34 OUT LVCMOS25
E_KEY0_FPGA D15 INOUT LVCMOS25
E_KEY1_FPGA C15 INOUT LVCMOS25
E_KEY2_FPGA G12 INOUT LVCMOS25
E_KEY3_FPGA H13 INOUT LVCMOS25
CUSTOM0_FPGA_IO F15 OUT LVCMOS25
CUSTOM1_FPGA_IO AW16 OUT LVCMOS25

AVR_RXD and AVR_TXD are UART links RX and TX between the FPGA and the AVR.
The other pins are either GPIO pins or a SPI link between the FPGA and the AVR. There is also no code on the AVR that uses these pins.