I'm not familiar with CTC printers, but there certainly could be an issue with the missing temperature sensor for the right-side extruder if the printer firmware is expecting it to be there. Is there a control panel or firmware means to disable the second extruder?

I'm finding conflicting information on whether CTC printers use a thermistor on the hot end or a thermocouple. If it uses a thermistor, the thermistor resistance goes up with temperature. If the thermistor isn't there, it is as if the thermistor is very high resistance, or reading a very high temperature. This would result in the overtemp error. That, however, would be an error I'd expect the printer to have right away, not waiting until mid-print.

If your printer uses a thermocouple, then maybe that thermocouple input on your electronics is floating around with nothing connected to it, and the electronics eventually picks up a higher voltage on it than normal, tripping the temperature error.

The easiest path forward is likely to connect at least the temp sensor part of the right-side extruder to your electronics.