It looks like you’ve received some great advice! I thought I would add some ideas that I’ve used in the past. I found an injured kitten in my yard about 3 years ago, and she holed up in a bedroom and buried herself behind a pile of pillows. She hissed everytime she saw me. It took a long time for her to engage with me, but here’s what I did.
1. Anytime I reached for her, I moved my hand slowly, didn’t look directly at her, and kept my fingers tucked in. I figured this was more like I had my ‘claws’ retracted. I only reached for her when I had to (like when we had to go to the vet for checkups on her injury, or when I had to bring her into the open for food).
2. I always greeted her when I came into the room. Soft voice, but used her name and asked her how she was feeling…told her how beautiful and strong she was…yada yada yada.
3. I would go into the room both when I had to interact with her, and also when I didn’t have to. When I didn’t have to touch her for some reason, I would just take a book or my DS in with me and lay down and just hang out for a couple of hours at a time. Then I would leave. That way she didn’t associate my presence with some kind of forceful action. You know…sometimes I’m just there.
4. This one is the toughest, but I think probably the most important. Fake it. If you are stressed out, they are going to pick up on it. Just make yourself be normal, like nothing is wrong.
As for the litter box problem, I would add more litter boxes. It’s just temporary, but this is what I do every time I’ve brought a new cat in. I put litter boxes in every area of the house.
And the only reason I had my girl confined to her own room was because she was injured and I have other cats. I didn’t want them to scare her or mess with her while she was healing. Otherwise, I let the cats (new and old) have the run of the house. I figure this gives them more space to choose their own ‘safe zones’. But that’s just me.
Now, my girl is a big ole lap cat. She even sleeps under the covers with me. It took a long time, and she still doesn’t totally trust my husband, so I know all this stuff helped her know that I’m her person.
You’ll get there, it’ll just take some time.