One way to find out if that ductwork is also going to your neighbor's apartment might be to close your vents, turn off the heat and turn on the fan, and place a stink bomb (egg and vinegar, see http://www.wikihow.com/Make-an-Assortment-of-Stink-Bombs) in the exhaust draft.

I have scheduled sandblasting, then boric acid and vinegar spray followed by paint wood joists subfloor below, and Drylok supreme along the foundation wall. 

Work out more, I got a lot less flak from everyone once I hit 190lbs of piss and vinegar.  

Then bought the Simple Solution, but couldn't tell if it needed to be watered down or sprayed directly or what (it was a gallon jug), so I called them and they said dog pee, specifically, dries to an alkali, and to bring the Ph level back closer to neutral would help the enzyme work better, so they advised to spray a white vinegar/water 50/50 solution on the pee spots and then let it dry.  

I instructed the tenant to take down all the curtains and wash in hot water with vinegar.

If it was me, I would shampoo the carpet with ammonia and then vinegar, I would wipe down all the hard surfaces with ammonia and then vinegar, ceiling tiles I would either repaint or replace. 

They would also put bowls of white vinegar around the house, and the smell would be gone very quickly. 

We mopped the slab and walls with  white vinegar, gallons of it, several times, to neutralize the odor, then washed everything down with TSP, then used original Kilz over the worst areas. 

I washed the walls with a urine gone solution and vinegar.

If a porous surface, clean with a vinegar mixture (half water/half vinegar).