Our female came to us last year as a timid little girl. She is 10 years old. She was not spayed and would hide, or run when myself or my husband walked by.. it took a year for her to finally just get used to us. We learned that she doesn't like my husband in dark colours,especially his blue robe. She was spayed last year and is a little more relaxed.
We learned to walk slowly and let her pass, to get to her level as much as we can, and to let her take her time to make some changes and to trust us.
I think it will take us a few more years for her to fully trust us and not feel so timid. I'm willing to wait!!
I really think that you just need to take what she can give, and try daily to give her a little more cuddles but on her terms, whatever that may be.
Maybe if you have her spayed she will chill out a little, as ours did.
Your story sounds so much like ours. I have faith that she just needs a lot of patience as our Millie did. You'll see. The more you get to know her, you'll notice certain times when she is more apt to allow you to get close.
You'll be rewarded!!