ATMega 32u4 standalone pins

im currently making a custom pcb with a 32u4 as the controller, which i migrated over from a pro micro. when i look at the schematic of the pro micro, i see that digital pins 11-13 are marked as "not used", but it seems they still have a designation in the arduino ide (i think). can i use these pins for my project or will these pins be inaccesible because im using the pro micro bootloader?

If the pins are not currently selectable, you can look at boards.txt and the version of pins_arduino.h to see how the pins are created and modify it to add them in.

CrossRoads:
If the pins are not currently selectable, you can look at boards.txt and the version of pins_arduino.h to see how the pins are created and modify it to add them in.

i am going to be completely honest here and say that i understood maybe half of that

The ATMega32u4 is the basis of the Leonardo, which has support for pins 11-13. I can't see why they wouldn't be available if you're making your own board and you route them out. I don't know the history of the Pro Micro but I assume they tried to keep the form factor of the pro mini which uses the ATmega328. Since the ATmega328 has 32 pins and the ATMega32u4 has 44, a few pins had to go if they wanted to keep the same form factor and header spacings.

Here is the boards.txt entry for the Leonardo:

##############################################################


leonardo.name=Arduino Leonardo
leonardo.vid.0=0x2341
leonardo.pid.0=0x0036
leonardo.vid.1=0x2341
leonardo.pid.1=0x8036
leonardo.vid.2=0x2A03
leonardo.pid.2=0x0036
leonardo.vid.3=0x2A03
leonardo.pid.3=0x8036


leonardo.upload.tool=avrdude
leonardo.upload.protocol=avr109
leonardo.upload.maximum_size=28672
leonardo.upload.maximum_data_size=2560
leonardo.upload.speed=57600
leonardo.upload.disable_flushing=true
leonardo.upload.use_1200bps_touch=true
leonardo.upload.wait_for_upload_port=true


leonardo.bootloader.tool=avrdude
leonardo.bootloader.low_fuses=0xff
leonardo.bootloader.high_fuses=0xd8
leonardo.bootloader.extended_fuses=0xcb
leonardo.bootloader.file=caterina/Caterina-Leonardo.hex
leonardo.bootloader.unlock_bits=0x3F
leonardo.bootloader.lock_bits=0x2F


leonardo.build.mcu=atmega32u4
leonardo.build.f_cpu=16000000L
leonardo.build.vid=0x2341
leonardo.build.pid=0x8036
leonardo.build.usb_product="Arduino Leonardo"
leonardo.build.board=AVR_LEONARDO
leonardo.build.core=arduino
leonardo.build.variant=leonardo
leonardo.build.extra_flags={build.usb_flags}

You can see the build variant is "leonardo"
These are the pins to names from the variant/leonardo/pins_ardiuno.h:

const uint8_t PROGMEM digital_pin_to_port_PGM[] = {
	PD, // D0 - PD2
	PD, // D1 - PD3
	PD, // D2 - PD1
	PD, // D3 - PD0
	PD, // D4 - PD4
	PC, // D5 - PC6
	PD, // D6 - PD7
	PE, // D7 - PE6
	
	PB, // D8 - PB4
	PB, // D9 - PB5
	PB, // D10 - PB6
	PB, // D11 - PB7
	PD, // D12 - PD6
	PC, // D13 - PC7
	
	PB,  // D14 - MISO - PB3
	PB,  // D15 - SCK - PB1
	PB,  // D16 - MOSI - PB2
	PB,  // D17 - SS - PB0
	
	PF, // D18 - A0 - PF7
	PF, // D19 - A1 - PF6
	PF, // D20 - A2 - PF5
	PF, // D21 - A3 - PF4
	PF, // D22 - A4 - PF1
	PF, // D23 - A5 - PF0
	
	PD, // D24 / D4 - A6 - PD4
	PD, // D25 / D6 - A7 - PD7
	PB, // D26 / D8 - A8 - PB4
	PB, // D27 / D9 - A9 - PB5
	PB, // D28 / D10 - A10 - PB6
	PD, // D29 / D12 - A11 - PD6
	PD, // D30 / TX Led - PD5
};

Is it missing pins? The file can be modified and the missing pins added. They need to be described in several places in the file to fully document them.