i have an infared temp sensor and could not get consistant readings on the headers because of the point previously mentioned. best results for me occured when i managed to get temp off the exhaust collars. it was more of a curiosity thing; all four pipes had felt evenly hot to my uncalibrated fingers and the plugs looked tan after plug chops at various rpm's. called it good enough.
but to consider your question.
before i would tweak the idle, needle and main jetting only based on exhaust temp, i'd confirm across each carb: equal cyl compression, airflow thru the head pathway from carb to exhaust, spark quality, spark timing, valve and seat condition, valve adjustment, valve guide condition, equal flow thru each carb circuit (idle, needle and main jets), carb settings and zero vacuum leaks.