We are in the process of applying for ISO 17025 accreditation and I am trying to create uncertainty budgets for the calibrations that we do on infrared thermometers.
Question that I have is, other than the uncertainty of the two thermometers that are being compaired (UUT and reference) what other components should I take into account?

Linearity, Bias, Repeatability, Reproducibility, Resolution any environmental factors which may effect measurements, pressure, humidity, etc....depending on what application you're using the instrument in you can get highly detailed or stay with core items, depends on what you want really.