I was in your position a week ago! I smelled it for a few weeks in our computer room. I scrubbed walls, carpets, re-scrubbed the litter box... Finally went away after I cleaned under the furniture. I think kitty may have sprayed under a side table by our TV. He never sprays in the computer room (which is his feeding/litter box room). For some reason, he only sprays when it is raining and the dog tracks in stuff near the back door.. it's tile so not so bad. That only happens a few times a year though.
If you have access to a black light, you can turn off the lights in that room and the pee will show up. My DH did that in our house in Ohio, after two females had a peeing war while we were on vacation. We ended up having to remove all of the carpet in a couple of rooms, shellac the floors (it will seal the smell), then put in pergo wood floors. We finally had to separate the cats. There is nothing worse than cat pee in the house!
Our house in KY is almost all wood floors. I will never have all carpet again.