I brought a feral kitten home that wanted nothing to do with me and was so frightened that she spent a majority of her time hiding in my closet. She would only come out at night to eat and use the litterbox (or when I wasn't in the room, I assume).

What I did was confined her to one room (my bedroom) and at the time I actually spent quite a bit of time in my bedroom. So I would come home and hang out on the computer or do whatever and I just "ignored" her. Soon, I would wake up at night to her curled up next to me on the bed, only to be gone hiding in the closet again by the next morning. Eventually she would start to come out and play at night when I was on the computer, but would run and hide if I stood up or moved.

And after a little bit (a month or so), she and I became inseparable and formed such a bond that I have yet to find again in any pet. She spent every minute of the day that we were together touching me in some way, and she was not warmed up to anyone else in the house, only me. When my BF moved up here I was quite surprised to see her immediately take to him, too.

Sadly, we had to say goodbye much too soon (I had only had her 8 months; she was maybe 1 1/2 years old) as I lost her to kidney disease

Do not force yourself on her. Take things slowly and work with her at your pace. Give her a little time. You may just be amazed at what happens.

As for the litterbox issue... how may cats do you have in the house? How many litterboxes do you have? How many levels are in your house? Has she been to the vet recently?

I absolutely agree with keeping her confined to a smaller area and not giving her too much freedom too soon.