An IR gun? You'd be a bit lucky. There's no way it would give you sensible readings trying to measure some metal with a vastly changing stream of gas flowing through it on the other side.
Best way is of course with a decent exposed probe (enclosed ones are too slow to react) welded to the pipe 4-6" away from the piston. Then you work out how hot it is getting, but guessed figure measurement is only ballpark, - best thing is to dyno it changing jets to find the best power & record the temp it achieved. Then you can alter jetting for changing conditions to achieve that same temp.
Sounds like too much work for an enduro/trail bike. Just a dyno session with an old road spooned on would give you main jet size close enough for most use if you wanted to be that sure.
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