Background: The HVAC unit I have serves both the 1st and second floor, but does a poor job of distributing heat to the 1st floor. The previous owner added a hydrodronic boiler and baseboards to the 1st floor, so the duct vents for the 1st floor are closed and sealed (with magnetic covers and some duct tape).
Problem: My HVAC unit is located on the 1st floor and when the upstairs T-stat calls for heat I can hear a fan kick in for about 15-20 seconds before the poof/rawr of the burner lighting. During this time there isn't a smell, but shortly after lighting another fan kicks in making a clacking noise (you can hear it here). A minute or two after this I start to smell something earthy akin to burning aluminium, or maybe a strange mold. The smell is most prominent just out side of the equipment room (even more than in the equipment room itself) and isn't nearly as bad on the 2nd floor. What might be causing the smell? the clacking noise?
Possibly related info: There seems to be two sets of fans associated with my heater. When it first kicks on, a fan, that I'm guessing provides the air supply for the burner starts up and begins drawing air though a grates on the side and top of the side of the furnaces burner compartment. About 45 seconds later another fan that has starts up, and begins circulating air though the system, however, at the same time, the same slots that were previously drawing air in now begins to blow air outward. Might this be part of it?
Video of one panel removed, before and after the second fan kicking in: https://photos.app.goo.gl/CgdhcCxrmfskzMjZA
And another clip better demonstrating the force of the air flow after the second fan kicks in: https://photos.app.goo.gl/pdEWUi4Q39MHwkLB6
The triangular grated thing next to the motor connects to the flue, and it's ability to draw in exhaust doesn't seem to be affected by the second fan (though this might change once the paneling is back on).