I don't have much help to offer either.
What about her food, could that be having an impact? (Probably a silly question to ask, but you never know)
For your carpet though, Nature's Miracle works *really* well. Trust me, it *will* remove those poop stains. My cat Samson had some soft stools the other day and he "scooched" himself on the carpet in an effort to clean himself (I was asleep at the time) and he left me several lovely trails of nasty poop, and a lot of it too. The NM's took complete care of it. All the stains are gone.
All you have to do is shake bottle well, apply generously, work it in vigorously with your fingers (I always wear rubber gloves) and that's it you are done. No need to do anything else. The only thing I do is with a paper towel, I absorb the excess foam of the NM's as it changes color so it does not soak back in the carpet. Occasionally I have to reapply a second time, but very rarely.
Hugs to you and your sweet kitty