Kilz, vinegar, bleach, paint, and an ozone generator should be some great tools to attack the problem. 

@Diana Dorantes use honey more than vinegar.

For urine odors, tons of  white vinegar can neutralize it. 

The interior wall surfaces are all tongue and groove boards (cedar), there are visible nicotine stains on the air returns.Every single surface will need to be cleaned in some capacity, but I am left scratching my head at effective solutions.I've found a few anecdotal recommendations about using white vinegar or TrisodiumPhosphate, but when you need to scrub the walls and the ceilings of a 1700+ sqft house that seems pretty daunting and time consuming given that it is tongue and groove.

The best treatment for gnats is a bowl of apple cider vinegar. 

You catch more flies with honey than vinegar.

I gave them the solution (baking soda, white vinegar, water) for this and handled it myself.

I have seen remedies ranging from setting out bowls of vinegar to complete gut.  

You’ve never heard that you can catch more flies with honey than vinegar?

The best cleaner though SHAW is voiding warranties for using it is a half cup of white vinegar in a gallon of warm water and then a cool rinse.