I am at my wit's end with these animals! Fluffy, our 9 year old persian, got some sort of infection. I can't remember what the doctor called it, but she compared it to the Mexican Two Step (if you drink the water in Mexico, you'll always be two steps away from the bathroom). We found this out because she was going potty outside of the litter box and it was loose and had blood in it. Anyway, she's on meds and doing better, but it's like she's forgotten where her litterbox is. We come every day to poop presents all over the house! I can't take it! What can I do to get her back to the litterbox??
Have you thought about leaving her in a large crate when you leave the house? I did that with Sheba when I took her to my sister's house. I borrowed a crate that was large enough to hold a litter box, a nice cat bed, and some food and water. It worked very well for us.
Can you lock her in a bathroom with the litterbox during the day until she "remembers" to use it? If it was coccidia, be sure to disinfect the box.
Like the others suggested, put her in a small area with the box. She wouldn't be having the run of the house til she got herself under control. Molly is now back to sleeping in the crate at night because the DR in not an acceptable substitute for outside in the middle of the night. :?
buy a new box to replace the current one and/or change the litter (brand) and/or change it to a new location. If defecating was painful or unpleasant for her while she was sick, she may associate that pain with the litter box. If you change one or more parameters to something she wont associate with pain/discomfort then she will hopefully go back to using it. Cats also have a tendency to want to "tell you" when something is bothering them by acting out like that, but it sounds like you are/have already worked on that