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As someone mentioned, a spot of flat black paint will help to neutralize the emissivity issue. We always did that on the dyno at my former employer. Anywhere that we were likely to want an IR temp reading off of got a flat black spot.
Thermocouples drift with age, they aren't absolute. RTD's tend to perform more consistently over a long time span.
Weld the junction together and you won't get corrosion and the drift it causes. In fact you can even weld the wires to what you want to measure the temp of.
I was told by our MS-EE who was in charge of the dyno & it's data acquisition system that it happens even with the welded wires. It's unavoidable, but it is a long term effect.