One of the main reasons a cat does not use their litter box is because of a UTI (as Jen mentioned). First, you should make sure she doesn't have this infection by visiting the vet.

Also, your cat probably associated the litter box with pain because of her last illness. Maybe you need to get a different type of litter box or multiple boxes for each floor of the house.

Also, make sure you clean the soiled areas well since the cat will return to the area that she soiled. If necessary, get a black light and that will show you if you cleaned the spot properly.

Another suggestion, if she is using one area, like the rug, try putting her food dish at that spot. A cat will not likely go to the washroom where her food is located.

But before all these suggestion, see the vet!