The measured temperature of the extruder ended up being about 40 degrees lower than what the machine was reading. I remembered the manufacturer of the thermocouple chip warning about stray offsets each time another junction is made, such as if the thermocouple wire connects to a terminal block. CTC had crimped horseshoe connectors on the thermocouple wire so those were cut off, the wire stripped, and a more direct connection made to the control board. That brought the thermocouple to a 20 degree difference. I suppose that if I remove the terminal block on the board and do a direct solder connection then the value will improve but I think I can work with this.