This isn't so much advice as a shared experience that might give you some insight into your situation.

Since your kitty was a stray, there's a chance that she was born feral, which would mean that she was born into a family that was no longer reliant on humans directly and therefore timid around them. My female cat, Jezebel, was a feral kitten rescued from below zero weather basically as a newborn. Today she is almost 13 and still very wary of people. She spent her first few years with us basically living under the kitchen table (if ever we approached her, even slowly and very gently, she would run under the table as if for protection.). While now she's much better--she sits near us, and even requests to sit in my lap if I'm sitting on the floor and she feels safe--it did take time. Like your kitty, Jezzy had a sister with whom she felt completely safe, and they played and groomed each other all the time. And Jezebel is quite comfortable showing her place amongst other cats, too. I also used to feel sad about how freigtened she appeared of us and of people in general. I worried a lot about her. But then I did some reading on feral cats, and realized that she's basically wired to be wary/skittish around people. That's helped me understand, and feel better about her hiding behavior, and I've tried to work with it on her terms. If your kitty is in fact feral, time may very well be what she needs to lessen her apprehension.