I just read your thread. Interesting arc. Your WW falls into a category that I sometimes think of as "unlikely cheater". Cheating isn't generally logical. That is the difficulty in trying to understand it. Understanding often involves attempting to impose a logical overlay upon a set of facts. But there are some threads where the psychological path to cheating is a bit more clear. Maybe not "logical" in that choosing to betray a solemn promise made to a spouse is generally not a logical decision, but at least understandable in human terms.
Not so much with your WW. Hence the concept of "unlikely cheater". What you see in some cheating threads -- and I'll risk being called sexist here to say that this appears more often in cheating wife threads than cheating husband threads -- is a woman who enters into a vortex of some species of self-loathing. Usually it comes at a time when she is aware of having aged. The cheating isn't really cake eating. Rather, it's a subconscious palliative to attempt to quell the spiraling self-esteem. Even that, alone, is generally not enough to catalyze the actual cheating. In most cases, she would pass through that phase marriage intact. Rather, what one sees is that the actual cheating coalesced within a "perfect storm" assemblage of vectors: the low self esteem, the goading friend, the new environment, the opportunistic scumbag who utters the saccharine words, all of which is neatly compartmentalized away from the marriage. The confluence of these vectors at one point is so unlikely that virtually minutes earlier or later and it would never have happened. I've seen so many threads where WW's in these types of affairs truly do not know why they cheated. It's almost as if they watched it happen in the third person. In hindsight, the overwhelming sentiment is: "How could I be so stupid?!?"
In your WW's case, your mugging and her subsequent suspicion that the AP was behind it served as a catharsis to get her out of her head, otherwise it may have gone on longer. Have you asked her about that? Also, have you ever brought up the fact that you're not sanguine her written timeline is actually complete? For example, you expressed at one point that you believe she gave the AP a bj in the gym. And there is the question of gonorrhea and whether any/all of their sex was unprotected. FWIW, in the vast majority of threads, most or all adulterous sex is unprotected.
I would add something else. There is an element of "found out much later" to your thread. Often, one aspect of healing is the quality of the marriage between the end of the A and the Dday. In your case, I gather the marriage was good during that time frame. It matters.
As to your personal journey, I can appreciate and understand how you got to where you are. My trajectory was somewhat similar to yours, with the obverse ending. My "bodygard" was a boy around age 10 at the time of my Dday and subsequent break-up of the family. In my case, like yours, my ex remained in my life because of co-parenting. We didn't share a residence, but over time the relationship with the ex achieved a certain equilibrium and even fondness and affection. We even did some "family" stuff with the young-un. Ski trips, amusement parks, etc. At one point she made overtures about possibly reconciling. "I'd never give anybody the chance to do that to me twice," was my answer on that day. In hindsight, I might have given a different answer on a different day.
I think I gave the answer that I gave because I wasn't convinced that my ex had changed. I actually did fear a risk of recidivism because it did not appear that she had achieved any meaningful insight on what led her to cheat. I felt it would just be setting myself up for more of the same.
In your case, it does feel as if your WW has made herself into somebody new, a better version of who she was. I wish you luck.
By the way, the AP coming by to apologize, that's rich. I've endured a few 12-step "non-pologies" over the years. They're meaningless. Done to make the apologizer feel good about himself.