Ammonia like smell from HVAC

it sounds like you may have a clogged hvac system. if there is a cabin air filter you can check that as they get clogged, also a rodent nest under the cowl panel is possible as they like to nest in the air intake for the hvac but usually there will be a smell. I would check under the cowl cover and see if there is a problem with the air intake first off.

1 filter. You could also try spraying deodorizer into the cabin air system intake near the hood and windshield from the exterior.

sounds like a mouse nest in hvac system, no smell because when using ac it doesn't use outside air, probably a nest on the screen at the hvac air intake or if you have a a cabin air filter check in there. many times rodents make nests have babies and then the car moves and they cannot feed the babies and so they die and rot smell comes into car. usually it is not hard to access because there should be a screen between the outside and inside under the cowl cover, if no screen and the little buggers vot into your hvac duct system this could be a much bigger problem entailing removal of dash completely. most likely this isn't the case, good luck

That would be antifreeze check radiator for coolant and if you have heat then check thermostat if equipped with one

The condensation is not completely draining. You may want to see if it is plugged. Find the drain area in the engine compartment on the bottom of the firewall. Use an air compressor to blow air back through to clear it. I had a problem with that area which was a ford expedition design flaw. It was draining onto my O2 Sensor and damaging it. I had to make a bypass with a part form a GM truck.

do you get heat out of any other positions,and is it cold ,warm or hot with engine fully warmed up? smell your getting is most likely anti freeze burning off of hot engine parts,either from leftover splash from the rad job or something let loose ,such as hose connection or other part leaking which is being drawn into the cabin thru the fresh air inlet near the wiper arms upper screen area (where car hvac gets fresh air)

I don't list a cabin filter available for 2007 - 2009 Explorer.
Usually the smell is trapped water in the hvac box due to a plugged drain line. The water is supposed to drain onto the ground under the truck when the ac is on.

Try the auto parts store for some stuff to spay into the vents to freshen it up.
mold, mildew could be present from the clogged hose

What your smelling is most likely coolant (antifreeze). You may have a heater core leak. If you dont smell the same smell after running the A/C or just vented cool air from outside for a few minutes then that is your problem.