I managed to reconnect my various little bits back onto my Raspberry Pi 5’s GPIO pins, using the special upright connector that reproduces the GPIO pins off to the right, in the same order as if you’re working directly with the GPIO pins. I’d found the schematic of the M.2 Hat+ and it appears that all the Hat is using on the GPIO are the power pins and pins 27 and 28 for the EEPROM on the board. All other signals appear to be coming across the PCIe cable. Since I’m not interested in the EEPROM communication pins I’m good to go.

Links

• Raspberry Pi Pinout — https://pinout.xyz/
• M.2 Hat+ Documentation — https://www.raspberrypi.com/documentation/accessories/m2-hat-plus.html