[donk.]

Improperly balanced / some HVAC system need seasonal adjustments
Furnace location does not matter unless you have 20ft of uninsulated ductwork dumping heat

I would close off the third floor vents by 30%, try it a couple of days, close more off if needed

Suggested to open the same amount elsewhere, if possible

Keep in mind, this may cause issues if you have AC built in, as summer will most likely require more airflow for the top of the house
Additionally, you may cause drafts, as closing off 3rd floor, and opening 2nd, will increase CFM


Closing off too much air, will reduce airflow across the HX, it may operate fine, it may stress it due to low airflow. If the burners are turning on/off constantly, you know you have reduced the airflow too much

Hard to say without knowing for sure

Thats the short version, goodluck you homeowner baller