It was lovely reading about Newt's progress and the kittens
I think it's all a matter of time. I tend to over think things too (but that's only because you want the best for Newt). But think about it, even when she's used to the outdoors and freedom she'll always have a warm place, food, shelter and love for her. I've been experiencing that with Bobandy my new family member who came from outside as well.
I think it's all a matter of time and patience. Does she like to play with you? Just you and her and a little string? Maybe providing some entertainment indoors will ease the boredom for her.
It's adorable that you take her for walks on a harness. It's remarkable that she got used to it so soon as a grown kitty. You must be doing an awesome job with them.