Keeping in mind some of the things from that post, like that I am unable to replace the floor and reading over the things I have tried cleaning with, here is an update.
There are a couple spots where I know she usually goes to when she does go on the carpet. She has only gone maybe 2-3 times inside since I wrote the post (usually between the hours of 3am and 7am even though she usually gets to go outside just before and after those times). I have used Natures Miracle on these spots, and have also gotten a blacklight to look around for more.
However, I'm concerned that even if I can get the odor out of the larger areas where she used to tend to go, I can see the neon stains under the blacklight just about everywhere. I imagine it's from steam cleaning the carpet every weekend for a while (bad for the carpet, but what else could I do!) and also possibly from her or stepping on a pee spot and then walking on the carpet to get to whatever we'd use to clean it up.
Any advice for large area clean-up? It doesn't cover any areas anymore, just little tiny dots on what seems like every other inch of the carpet. I'm afraid that without getting all of this up, the odor will never really go away.