As I've previously stated, I am remaking the electronics of the machine.
Going from two to one MCU eliminates the need for synchronization between the two boards and vastly simplifies the programming and updating of the code.
Unfortunately this also means I've lost almost half of my input/output pins.
To bypass this I've started using 74HC595 and CD4021B shift-registers which only require three pins each for any number (within reason) of input/output pins. The new boards will therefore handle 64 inputs and 96 outputs, with additional pins just being another daisy chained card after the first.
But the work behind these cards is immense!
Since I'm using regular experiment solderboards I need to solder wires or components from each pin to the next, causing the the switch-board alone to have around 500 solderpoints!
If I would be using an online service known as Pad2Pad or BatchPCB I could have made custom PCB's instead, but I'm currently going about it this in a "I'll do that if these boards break"-kind of way...
Hopefully I won't live to regret this!