Feliway can help with nervous cats and depending on what is causing the litter box issues, it might help with that. I'm assuming she is fixed, if not having her altered could help. If she was a true feral it will take a long time for her to ever get really comfortable with humans. Is she curious about you? Will she stay in the same room with you? Does she meow? If so, then she just needs time and a little pressure...she has to take treats from your hand or allow you to pet before she gets fed. As for the litter box, if she is spraying, it's territorial and she needs to feel safe and/or cats are spraying outside and she is marking her territory. If a cat goes to the litter box and it hurts, they will avoid in the future. If they can smell where a cat/dog/human has went before, they will cover which makes cleaning up with an oxy or enzyme cleaner vitally important. I currently have 7 cats, one of them has to have a covered box, the rest prefer open. A box must be big enough for the cat and if other cats attack one while using the box, they will avoid the box in the future. I have read about kenneling cats to retrain them to use a box, it takes about 2 weeks and if you think it might help, there is a lot of info on line. If I could determine which one uses the throw rug now and then, I might try it. I think I know and I truly wonder if he is developing a form of kitty Alzheimer's. Good luck.