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Usually furnace temp are mesured with thermocouples (just search "kiln thermocouple" on google, it is usually type K)
but you could get away with thermistors on exhaust mesurements as they can go to aprox. 200F
You might be able to mesure radiated heat from window in burn pot with thermistor, but you must then calibrate the readings using the temp gun to get a calibration curve.
You might also want to add a automotive LambdaProbe to the exhaust to mesure the completeness of the burning:
David.