Pick new "daughter board" connection parts. Likely copy what Arduino boards use to connect daughter boards. Think of using different numbers of pins arrange asymmetrically so that there is only one way to mate the two boards.
This is completed in the single board version (SB3) we're now using. It uses a smaller, keyed connector to connect to the switches, USB jack and LEDs that are externally accessible.
Pick new "daughter board" connection parts. Likely copy what Arduino boards use to connect daughter boards. Think of using different numbers of pins arrange asymmetrically so that there is only one way to mate the two boards.