The fact that she is using the litter box for stool and mainly having her problems with urination somewhat rules out a litter box aversion. But......she may have developed a substrate preference for urination. If the same litter is being used in all of the boxes, I would experiment with that first. Offer a litter box buffet for her to choose and when she starts using one for urine, then we will know if she prefers something different when urinating. Offer different types of litter, different types of litter boxes (short sided, tall sided, and different amount of litter in the boxes). You must scoop daily! Cat's are very texture specific so look at the places she is choosing to go. If it is a carpet, you may want to put a piece of scrap carpeting in a litter box for her and slowly add more litter as she starts to use it etc). Some cats, mine included, prefer to urinate in an empty litter pan with no litter at all.
One other thing I would suggest is a product called Feliway®. LINK HERE Feliway is a synthetic pheromone that mimics the natural chemicals that a cat secretes. It creates a comforting, reassuring feeling that has a calming effect. It has been shown to decrease urine marking and spraying within 30 days with a 95% success rate. It is also calming to cats in stressful situations such as transport, hospitalization, veterinarian visits, boarding, new environments, pets or people. Feliway® is a product that can be sprayed or used as a room diffuser. It can be purchased through veterinarians and pet stores. I would definitely put a few of these around the house.
Environmental enrichment has become a very important subject in feline veterinarian medicine as we have now identified that many cat behavior and medical disorders stem from the fact that they are confined indoors and forced to share territory with other cats and humans, which is not how cats naturally choose to live. This "stress" can lead to physical and behavioral problems. There is a website I am including the link to that addresses this subject in detail and offers suggestions to modify her environment to offer her a safe haven where she can hang out if she feels stressed and offers other ideas of how to interact with her.
Finally, I was just at a veterinary conference where I was introduced to 2 supplements for cats that have been clinically shown to reduce anxiety and tension. These would need to be ordered by her veterinarian, but there are case studies that show these products to be helpful in these kinds of situations. Here are the links:\
I hope this is helpful. Please let me know if you have ANY other questions. My goal is to give you 100% satisfaction and if you are not yet satisfied, please reply so I can clarify for you.
My posted replies are for general education only and not meant as a diagnosis. Only after a thorough veterinary examination can a diagnosis for your pet be made and specific treatments be advised or medications be prescribed.