What general purpose connectors are used for GPIO data?
I usually go with Standard DB style (D-shell) connectors available in 9, 15 or 25 pin types. It's easy to get pre-made cables in a variety of lengths. You can go shielded or unshielded. You can get short ribbon cables that adapt your board (typically 0.1" IDC) to a DB connector that can be mounted to the chassis and then use a pre-made cable to connect the two boxes. Very robust.