1. Try adding a second litter box. Make sure one is in an area where she tends to go outside of the litter box and the other more secluded. 
2. add scratching posts and other activities for her. They make activity boards and other games for cats. try getting her to chase a laser
3. add the pheromone diffuser back in
4. visit the vet for prescription medication to help calm. prozac, amitriptyline etc. its time for some blood work/urinalysis to see if there is a medical reasoning behind her behavior. Try visiting a cat only hospital. There are feline friendly practioners!
5. try some of the prescription calming diets
6.  Look into a behaviorist that can come to the house and see the living situation in person. its easy for a bunch of strangers to suggest things without seeing the environment. 

good luck. its a tough situation