The cat had pissed under the couch and the tenants never cleaned it up, so it rotted through the carpet, subfloor, and the smell permeated into the floor joists.

(Sadly, Elon was more interested in the Twittersphere.)The way laws are written/enforced; it's almost impossible to prosecute and convict competent white-collar criminality, as the smart crooks have found all manner of ways of creating quasi-legitimate facades/presentations that play on people's gullibility and "greed"....this ethos permeates all sectors.

Lived in the house for 13 years and was a hoarder...the smoke permeated EVERYTHING ...

Even if they don't smoke inside or outside the property, the odor of smoke in their clothing gets inside and permeates the place.

In furtherance of such obligation, TENANT AGREES TO PERFORM THE FOLLOWING:1.To keep the Premises free from dirt and debris that can harbor mold;2.To inspect the Premises regularly for the indications and sources of indoor moisture;3.To immediately report to Landlord any discoloration evidenced on walls, floors, or ceiling and/or any water intrusion, such as plumbing leaks, drips or flooding;4.To not air dry wet clothes indoors;5.To always utilize stove hood vents when cooking items that may cause steam;6.When showering/bathing, to always utilize the bathroom fan and to notify Landlord of any nonworking fan;7.To water plants outdoors;8.To notify Landlord in writing of overflows from bathroom, kitchen or any other water source facilities, especially in cases where the overflow may have permeated walls, flooring or cabinets;9.TO IMMEDIATELY WIPE DOWN ANY WATER OR CONDENSATION THAT APPEARS AND/OR DEVELOPS ON ANY AREA OR ANY SURFACE;10.To clean upon first appearance, any mildew from condensation on window interiors, bathroom & kitchen walls, floor and/or ceilings.

If you don't have forced air circulating in the space, then put a space heater below the window.If the mold has permeated through the drywall, and is not just on a surface that can be cleaned, then you may need to replace the drywall.Check with your local utility company to see if they offer free energy audits.

Furthermore, marijuana has a very prominent and distinct oder which will permeate the house and can be rather difficult to remove.

I am wasting materials by getting PT Plywood but it is cheaper (not too worried about material cost in this situation, more for a better outcome).However, he stated we needed to avoid the "gap" so water doesn't permeate through the bottom level. 

Is it possible to remove the smell if it has permeated the structure?

I'm thinking about Imbue Property Management (Imbue: to inspire or permeate with a feeling or quality).