This de-waxed shellac solution eliminates the toughest odors—food, pet urine, cigarette smoke and more—and won’t yellow with age.

The tenant may start using candles.

I'll put several apple&cinnamon candles or better yet there are air fresheners that you twist and leave on different spots of the property.

At sale we got a roof, first floor wax ring, garage roof patched, and some other minor repairs.

You may have a bad wax ring and unstable toilet, since its below a bathroom, but also be aware that water will run down a vent pipe that goes through the roof, if the boot on the roof penetration is bad. 

They have everything you need in the box including the seat, wax ring and floor bolts.  

I like the "better than wax" seals because I don't like to get my hands sticky and they seem to hold up better to movement than wax.  

A hard wax oil like Odie’s Oil is a good option or a commercial grade waterbased finish like Loba Supra.

A couple of leak sources that the others have left out:* toilet tank bolts (these mount the tank to the bowl and rust out from water contact within the tank)* toilet tank gasket (gasket between tank and bowl)* toilet bowl wax ring* tub faucet handle escutcheon plates (water gets behind these plates and then gets behind the wall)

The seller covered it up by spraying air freshener and burning candles.