We bought a house that was previously inhabited by a cat breeder and her 35 cats... At the time we thought it was a great idea because we got an awesome deal on the house. Cat pee isn't that hard to get rid of, right??? WRONG!!! Almost a year later, we are still working on renovations, but have most of the smell under control. Here's what we had to do: tear out all baseboards, and as we replaced them, put lots of caulk between boards and wall so smell couldn't sneak through. All walls were primed with an oil-based Kilz odor-killing primer, then painted with 2 coats of regular paint. All floors were replaced- the subfloor is plywood, so dh painted that with primer before we put down our wood flooring and ceramic tiles. All that work wasn't enough---- our a/c and heat registers are in the floor, so the cats had been peeing in them. The airducts were full of old cat pee. So, dh replaced all the ductwork for the entire house. And there's still some smell. Dh said the smell is probably in the insulation within the air conditioning/heating unit. So, he is going to have an a/c person come out and take the unit apart and really clean inside and replace the insulation. We also had to take all the kitchen cabinets out because the particle board they are made from had actually swelled from being peed on so much. We tried to clean them but they still STANK. Gutting the kitchen was the only solution.
I'm sure you don't want/need to do a bunch of stuff like that; I just wanted to list a lot of the possibilities for smells... If you can find the source of the smell, I've heard washing the surface with vinegar might work. If you haven't had a cat for 2 years, I don't know where it could be coming from. Have you done any recent work on the house, where you'd be cutting into walls that might have been peed on? (for example, even after we painted our house, when we cut the door trim to fit the tiles under them, the smell was horrible because the pee had soaked into the wood). Or is there any way a cat from the neighborhood is somehow getting pee into your a/c system (I don't know how).
I know I'm probably not that helpful. But I did want to share my cat pee story (couldn't resist!) and tell you that I feel your pain!!! That's some nasty stuff!