@nottinghack After making these repairs, I wanted to test absolutely everything to be sure nothing else is about to blow.
I initially started simple, I connected the control box to a power supply, current draw was small and all the voltage lines looked OK.
Moving a little further, I wanted to make sure it could switch a load without issue, but I didn't want to do that with the POD attached in case of damage to that; looking at the circuit diagram for the control box, transistor 3 appears to connect from the coil of the power relay at the collector, and 0 volts at the emitter, with the base coming from the pod from a line named "RELAY DRIVE", so this must be how the pod can disable the motor.
A simple dupont wire between pins 1 (+5Va) and 7 (relay drive) on header X9 (POD connector) ensured the relay was always enabled, also shorting pins 4 and 5 on X6 (thermal cutout switch), then just adding a small 12v motor to the motor terminals, and shorting pins 5 and 6 (motor switch feed/return) on connector X8 resulted in the relay making a nice clear click and current draw at around half an amp - perfectly fine.
Then I just quickly popped the POD off and with some dupont wires connected it to the control box, with a 10k ohm resistor between pins 1 and 2 of X6 to simulate the thermocouple in a good state, and everything worked as expected, the POD LEDs behaved just as expected, showing full battery and low load.