I have now crimped 80 pins onto the ends of 40 cables. I've heat shrunk the each one to ensure no shorts and for things to look neat. I was also able to get all 80 wires through two 20mm holes in the enclosure and cut a perfectly aligned hole for the USB cable to fit through.
Next step is to now plug it all in and start testing what happens.
More cables will be required for Phase 2 including:
4 cables to the stepper motor
6 cables to 2 opto-interrupters
2 cables for external power
I'm planning to make custom moulded silicone grommets for the holes so everything remains nice and clean inside.