You might wish to look here:
http://www.dansmc.com/Spark_Plugs/Spark_Plugs_catalog.htmlAre your exhaust headers the stock double wall pipes? The way they are bent during manufacture, there is no guarantee that the inner makes full contact with the outer. In fact, that's kinda the point for double wall exhaust in the first place.
What was the ambient temp during the readings and was there a fan blowing on the motor? How long was the engine running, and was the choke off fully on all carbs?
What air filter are you using? Pods? If so, are they oiled equally?
Did you do a sanity check on the IR instrument and compare the pipe heat by flash touching the pipe? Did you measure the same relative point on each pipe? Were the readings consistent 5 inches away from your previous readings?
Did you double/ripple check instrument readings for consistency?
If spark timing, cylinder compression, valve adjustments, are all good and equal. Then that leaves carburation as the issue. Intake runner leaks aside, are all the carb adjustments equal?
Did you just rebuild the motor? New rings? Valves? What mileage on these parts?