Smells like a fried regulator. Can happen when the supply inputs are shorted by accident.
When I set SW3 to 5V, Vin is no longer 12 V. It is around 0.5 V.
What should I do to get the kit back up and working?
You have to replace the ICs one by one and then check on the kit whether there a short between short between Vcc and Ground exist before powering up the kit.