CTLady, you’ve already gotten tons of good advice from others, so I won’t repeat their suggestions. There are a couple of things I’d mention as being specific to this kitten’s situation, however.
First, if you can, I’d sit or lie on the floor when you’re in the room with the kitten; it’s less threatening, and makes you more approachable. (One room would be better than two.) At her young age, I’d start spending as much time in the same room with her as possible.
Start serving a tablespoon of wet food in a shallow bowl or plate on the floor, a few feet away from you (not within arm’s reach). After a day or two, start moving the bowl or plate closer to you. In a few days, the kitten should be eating while the bowl is next to you. Then you can try to pet her. Then switch to a scant tablespoon of plain, unsweetened yogurt. After a couple days, dip your fingers in it. Let her lick the yogurt off your fingers. This will help her learn that hands and fingers aren’t as scary as she first thought. Do this until she’s actively seeking out and sniffing your hands; reward her behavior with using her name in a happy tone of voice, and petting her (briefly).
Second, this kitten will never likely respond well to being ‘scruffed.’ However, that’s a standard veterinary technique used to help handle frightened or feral cats (used initially to control the cat while getting the other hand under the cat for supporting body weight). Your best bet is to choose never to have her handled in such a manner – and warn any vet she sees about this; indicate that her records should clearly indicate that scruffing is a technique not to be used on her.
However, should it be needed in the future, it’s wise to teach her how to tolerate it. (Preferably when she’s at the licking-yogurt-gladly-from-your-fingers stage, and thoroughly distracted from whatever else you’re doing to her.) While she’s licking up yogurt, go ahead and gently grasp the scruff of her neck; then let go, and pet her, use her name in a happy tone, and tell her how happy you are that she didn’t struggle. A bit of repetition, graduating to a firmer grasp and picking her up (while supporting her body weight with the other hand), and lots of praise and petting immediately afterward will probably go a long way toward helping her learn positive associations with being scruffed (and compensating against the conditioning of her earlier treatment).
She sounds as though she’s been rescued from a very bad situation, indeed. Bless you for helping her out! And good luck!