It almost sounds as if you read advice for couples who are reconciling/piecing, and thought it applied to a sitch with an affair. Some guys get it in their heads that they can live in-house separation and slowly they will get closer until they reconcile. I've never seen it work with a WW, b/c important issues get pushed aside (due to her refusal to cooperate).....and the betrayed H tries to adjust and settles in for what seems to be their new normal.
IMHO, your passivity is your biggest problem. I'm so glad you read the NMMNG book, and I hope you continue to refer to it for a long time. Although you feel you've made progress, I think some of your posts speak to how you struggle recognizing your passivity in the MR. You allow things to ride, in hopes it will all work itself out. That may be the better answer to many things, but not so much when you are in a M with a WW.
FWIW, I don't agree about the H having sex with a wayward who has not ended her affair and is still being secretive about her phone activity. It doesn't matter if she initiates it. It's not "okay, just as long as she initiates"......b/c WW's are deceivers and manipulators. As a WW who is engaging in some type of an affair, she can easily mislead her H, by being intimate with him. Having sex with her H while she lusts for OM.......is not her attempting to getting closer to reconciling. Here's what happens. She messes with his mindset and he starts thinking that things are getting back to normal. In his passivity, she is not required to follow a transparency plan, and she's not held accountable for her contacts with OM. Basically, she doesn't have to do anything she doesn't want, b/c she leads and her H follows. The wayward spouse should be required to work hard to retrieve their MR. The WW will take the easiest way around doing the hard work. These are some of the issues the H faces when the WW is not remorseful, doesn't end her A, and required to do the hard work.
I think you have mistaken some things as her "efforts" in getting closer. You would post that she was definitely showing effort........ but in what way was she showing effort? Spending time with you, being nicer, talking more, initiating sex? Until the WW is willing to be truthful........how does anything count as effort toward reconciling? It just seems superficial. IMHO. Was there ever an agreement about the two of you working together to save the M......or were you assuming she was putting effort into getting along better. The fact she wasn't ready to talk about the A, was not reason for you to wait around until she decided she was ready.......b/c some WW's are never "ready" to reveal the ugly truth.
From my observations, whenever the H acts as if he and his WW are working at getting closer to reconciling....(when she will not agree to cease all manner of contact with OM (or possibly new OM) and be completely transparent), it results in the H feeling confused and not really knowing where the MR stands. I've seen some who really try to convince themselves the sitch is slowly leading to R. Some are nice guys who tend to follow the WW's lead. You cannot compromise with a WW. You can't passively sit back and allow her to direct the MR, by letting her successfully initiate sex......or calling the shots where you sleep at night......or passively accepting her refusal to show her phone messages. (These are only some examples.)
It's true that you control only yourself. However, I am not talking about controlling your W. I am talking about your actions. Your WW lost respect for you b/c of your passivity. You will not gain her respect by continuing to show passivity in the relationship. Start making proactive decisions for your life.
((hugs))
It is not about what you feel should work in your M. It is about doing the work that gets the right results. Do what works!