There are easy ways of getting more I/O pins for any project; shift registers, I2C expanders, or ADCs will give you plenty of pins for whatever project you have in mind. All these require extra com… ...

Running out of GPIO pins? Learn how to connect multiple buttons to just one Arduino pin using clever wiring and resistor ...

Arduino is strictly bootloader, and a bootloader cannot change fuses. “How do I reconfigure the IDE so that I can use these additional two pins.” The same way you SHOULD use the other pins.