I know you've heard this before, but I'm gonna belabor the topic and say it again ... I think relationship counseling would help you both a lot.
It's time-consuming, can be expensive, and feels like a pain-in-the-butt - all true. But I disagree that "this would all come on its own" if only your wife felt the way you think she should. Communication is obviously one of your strong points, but people are all so different. Your wife might have battles within herself or communication barriers that you simply can't relate to. She might just not be able to figure out how to approach or act out her feelings.
I have found that specific "homework" exercises and being prompted by a third party has led to some epiphanies and, better yet, the use of communication tools and methods that my husband nor I realized before. It's taken several months of this counseling to be able to look back and appreciate those things.
So in this new plateau you're describing, maybe consider it.
The one thing she is clear about is that she will not do counselling. I have told her I think she needs it and we need it. I would settle for her doing some research and reading first. She isn't doing that either. She has made changes, but the best I can guess is that she is in some kind of denial and thinks the best way forward is to put it all in (yet another) box and carry on that way. And that might indeed be the best thing from her point of view. I was absolutely amazed when I told her something she'd said just after d-day, and she didn't remember saying it. I believe she didn't remember it. If that is the case there may well be a whole lot more that she doesn't remember, not only things she said and did to me, but feelings. I don't know if this is right but it would explain why she thinks it can all just kind of blow over if she just keeps her head out of the firing line for long enough. Maybe she is right that we can just box it up, but to me it seems that it is going to be necessary to deal head-on with some things. If there'd never been an affair then I would probably be feeling fantastic about where we are at. And I think she may think it is mostly about the sex, but that is in some ways the least of it. We have been together about 13.5 years now. For more than ten percent of that time, her main focus was deceiving me. Not just incidental lies but a serious, planned, organised project of deceiving me. Not just on her own but actually plotting with someone else to deceive me, devising ways to communicate that would not be traced. It consumed a huge amount of her energy when our children needed it and I needed it, and there were many occasions when it was obvious that I was being destroyed by the way she was behaving towards me even when I didn't know why. I just don't think that's something that can be boxed up and left in the attic. Even if it could in some logical way, it isn't emotionally possible for me to do that. Thanks for saying communication is a strong point for me. It isn't really true in this context though. I can communicate I guess but it is starting on the subject that is hard. It's draining. And because it all needs to be dealt with but she won't deal with it, I am always the one spoiling the day if I do bring it up.
Maybe it is okay, maybe it will be okay.
BS, d-day Feb 2017, 16 mth affair.