Stuck, I will make a couple of quotes and comments, and then I'll make a general statement to you about your sitch.
You said: "She begged to come back, so I let her back with the agreement that we were to work on the R. So while we're living together with our 2 kids, she gets angry at me all the time and refuses to talk to me about the R, saying that we can discuss it at C."
I know hindsight is 20/20 so you probably already realize that it was a mistake to let her come back with the agreement that you were to work on the R, only to have her refuse to talk about it later? Why did she beg to come back anyway? I'm just curious about that part. She was just afraid to find her own place or....?
You said: "So in mid-Dec. she agrees to move back home with them so we can take care of them together."
So this sounds like she agreed to come home because it would be more convenient to take care of the children together, but she never agreed to work on the R this time, correct?
You said: "Unfortunately she still works with the guy she had an EA with, but I do believe her this time when she says there's nothing going on. She comes home early, doesn't sneak around anymore like she did at the height of her EA. She still gets extremely defensive if the EA ever gets brought up (I think out of embarrasment and shame) and has never apologized to me for it since it wasn't physical."
I have to wonder, why do you think it wasn't physical? Because she said it wasn't? Also I have to wonder, did she and the OM have a formal "break up" or what? How did they stop their affair? If you don't have a lot of details about this, then how can you believe her that its over? Unless maybe there is some detail you've left out, like that he dumped her and you saw the evidence of it.
You said: "I don't know if she still has any residual feelings for her boss as she still won't talk to me about personal things. So how do I get the psychological sex switch turned back on after the WAW has turned it off?"
I'm going to take a guess here and tell you that you may not ever get it turned back on. It sounds to me like there is too much resistance on her part to reconcile with you. If she won't even talk about the R, still considers you two to be separated, only came back home because it was easier to help the kids....well, that doesn't sound like much hope. I don't mean to be a downer and maybe there is something that I have missed, but to me it sounds like she is just waiting this out and will leave again at her earliest opportunity. In the meantime, both you and she are in limbo and are unhappy.
I'm going to give you some straight up advice that you probably won't like: I think you should ask for a separation again, WITHOUT having any plan on working things out...and do NOT ask for counseling again, unless it is counseling for the children or the family together to prepare you for the pain of separation and possibly divorce. In other words, I think you should begin to move on, and that YOU should be steering the "moving on" ship by asking for the separation.
What you are doing right now, even though it is loving and courageous, is going to do nothing but continue to turn her off. You have allowed her to dictate what will and what will not happen during this whole thing (other than the inital throwing her out, which was the best thing I've read in your sitch so far). This has caused her to have no respect for you and for her to just feel that she is in control. Unfortunately, when a confused, frightened WAW is in control, you can expect the ship to toss and turn and probably end up shipwrecked.
If instead, you were to totally take control of steering this ship, then at the very minimum you can make sure it doesn't crash and your kids are protected as much as possible.
It is painful, yes I know. It is risky, yes that too. She may just say something like "oh GREAT, I WAS actually thinking we might be improving here and there might be a chance, but OH NO you have to go and ruin it, fine have your separation, we are DONE!" If she does say this, don't buy it. It will just be a reaction. From everything you are describing, she has no intention of trying to reconcile with you. So ... IMO ... the ONLY thing you might do that MIGHT cause her to want to reconcile is to pull the plug on her control and take it back.
I'm so sorry when I give advice like this because I so much want it to NOT be true. But when a WAW has it in her mind that she has all the control, then it is like a death sentence to her H and to the marriage. Try to keep in mind and remember that she doesn't actually WANT control of the ship. What she wants is to be happy but she is confused about how that can happen. She is convinced that being with you will not and is not making her happy. So...give her the opposite, for real this time. I know you were separated before, but I suspect she felt your presence hovering over her and wanting her back the whole time. This time, separate with the intention of moving on and you might get a different reaction from her.
And finally....
I don't buy it that the A wasn't physical. I also figure that the OM is a dirtbag and that the A will start up again at some point as long as she is still working there. And even if she changed jobs, her heart is still available, so another A will probably start up at the new job.
To me, the only tool you really have at your disposal, is in being able to take the power back IF you can stomach the risks involved.
Stuck I'm so sorry for your sitch. It makes me cry, really. How I wish that my ex-h had had the bright idea to do a DB plan or anything, as it would have worked on me. And it makes me so sad when some of these WAW's just don't seem to notice.
HOWEVER....having said that, Stuck you really must face your reality which seems to be telling you that she is willing to keep wiping her feet on you if you keep being willing to lay down and take it.
