There are several steps that need to be taken to determine what is going on with your kitty and get her feeling better-
First, she needs a veterinary exam. They can evaluate her skin and decide if she needs antibiotics. They can also perform a skin scrape to look for mange.
Next, she needs blood work and a urinalysis. The bloodwork is to check her liver, which, if diseased can cause skin problems, and the urinalysis is to look for an infection or blood in the urine. If any internal disease is found, that needs to be treated as well.
If no diseases are found on the exam and laboratory results, the next step is a diet change. The most common cause of skin problems in cats is a food allergy. I would recommend either a limited ingredient diet such as venison and green peas or a hydrolyzed protein diet such as Royal Canin HP. This may take a month to see results.
If the diet change doesn't work, you could consider allergy testing or steroids if we think that she is allergic to something in her environment.
Lastly, you need to remove the lid off the litter box. Cats don't like enclosed spaces for toileting because they feel vulnerable. They do like enclosed sleeping places, though, so you may consider adding a cat bed for her.
Does this help? What other questions do you have?