I would never point my IR thermometer at the end of the pull rod for the exchanger rake for starters.
As somewhat of an approximation I would put a thermocouple in the center of each (along with an air flow meter) air outlet and then you would discover that each tube gives a different reading for each device depending upon where in the line from the convection or combustion fan it is and how much crud is on the exchanger.
You also need to understand that the volume of air being pumped through each tube is different and that total heat produced is not a function of the temperature of a single spot on the stoves metal surface.
Find a book on heat transfer and bone up on differential equations.
If you cut the combustion air too low the stove could indeed go to overheat, it can also cause various parts to degrade such that they fail early and often. At the other end having too much combustion airflow can send a lot of heat up the flue.
You can measure what ever you want, but what you measure will not likely amount to the heat produced by the stove and further that temperature will slowly degrade as the stove cruds up.
If placed... What should it read?
I'll give ya a 20 point spread...
Smokey, I'm not trying to be a pain in the butt here, yet you have a good running stove right?
To give a baseline temp on what you're running, at any point of ease you wish.
What's it doing?