Thumos... sorry for your pain.
Here is my take after reading your story here.
You are in reconciliation and it is actually going pretty well in a number of areas. It has been several years but these things often take longer than that. Your description of your daily life is actually more positive than some other people who attempt reconciliation. I know it may not feel this way but that is actually a positive thing. The fact that you can laugh and enjoy yourself with her day-to-day most of the time is a good place to be at this point.
But it is also very clear that the poor steps taken after D-Day, particularly with the marital counseling advice, have left a number of unresolved issues for you. Unresolved issues aren't unusual. However, to have a full and rewarding reconciliation it makes sense to address them and not continue to rug sweep.
You know this is true. The question is, how do you move forward a bit differently to try to get some resolution?
You have described your wife as loving you and that she would be devastated if you left. Although she has rejected some of the tenants kept here on this site she has also demonstrated many of the behaviors of a wife who is really trying to heal her marriage. But early interactions shaped her thinking and blunted your action so you are left with an unhealthy Dynamic around some of these issues. Are you willing to try to open this dialog again?
I think you have leverage if she feels like you may still leave her and that is the last thing she wants to happen. You have to figure out how to use that Leverage to get her to see your perspective differently than she has up to now. You two have actually made a lot of progress in reconciliation even if it doesn't feel that way. I can't think of a reason why you wouldn't attempt to influence her with a different strategy to help yourself heal over these remaining stumbling blocks.
What do you think that you could do that would be different in approaching her at this time?
I really think you should answer the question above because we're not sure exactly how and when you last attempted to get these things resolved. But I could throw out a couple of possibilities to get your reaction.
First, I would set the stage that you need to have a serious conversation with her about the progress the two of you have made since D-Day. Don't jump right into the conversation but tell her you want to have that dialogue and it is very important to you. Ask her when would be a good time to have it. This way she will be prepared for the dialogue mentally and emotionally and of course so will you to the extent that that is possible.
I think it is important that when you ask for this interaction you make sure she understands the gravity of the conversation. Put it in an appropriately serious context. I wouldn't want her quite being so nervous that you're going to actually tell her you want a divorce yet I don't want her going into this conversation casually, thinking that she can say and do the same old things that have got you stuck on these issues. You might consider saying something like I think we have made great progress in our reconciliation. But as I think you understand, sometimes consciously or sometimes unconsciously, I am still struggling with several issues regarding your affair. These issues don't affect me constantly but they come up frequently enough and with enough intensity that they sometimes make me doubt I can continue to move forward. I am not saying I am unwilling to move forward, I actually want to. But these nagging issues have to be healed and are going to require some additional work even if it is uncomfortable for the two of us. All this gets said in advance of the time you're actually going to have the conversation so she is prepared to enter that conversation knowing your expectations. Does that make sense to you?
Another piece of preparation you might consider is defining some of the issues you are struggling with in writing ahead of time for her to read. Whatever those key issues are, you could write them out and get them in her hands so she has time to consider them and think about them deeply. Springing things onto her again in a dialogue will likely get her defense mechanisms up or she will revert back to her old tropes learned from the marital counselor and give you the same old line.
To offer up this time for her to prepare you also have to set expectations for the dialogue. How do you want her to interact with you? This is something you should Define very specifically for her. Tell her what behaviors you want to see when you discuss this and what behaviors you do not want to see. As an example, you might say that I really want you to consider my point of view deeply so that I feel really heard and you can challenge some of your preconceived notions about how we are interacting after the affair. What I don't want you to do is to go back to the same old arguments that have put me emotionally in a difficult place at times in the past several years. I need you to be open to taking some different actions because I have some unresolved issues and if you keep doing the exact same thing, they may never go away. And if I can't heal from them, it puts our reconciliation at some degree of risk. I think you can help me, if you are willing to think a bit differently.
The short version of what I wrote above is that you have to carefully prepare her to have a new dialogue and ask her to challenge what she's done in the past to help heal you more completely so the two of you can deepen your reconciliation and love for each other.
I actually think the way you have articulated your feelings here in this thread is excellent. And I know you've covered a lot of this ground in the past with her but sharing the most important priorities from what you've shared with us... again and a bit differently... is kind of a must-do, isn't it?
And you do want to prioritize your needs carefully. You might generate a list of five things she needs to address from either a behavior standpoint or a knowledge standpoint. And rank ordering them to know what are non-negotiables that you need to move forward verse is nice to have if she can do it would be important.
I have some other thoughts about how to actually have this dialogue with her. If you found the above comments helpful, ask me and I will write some more about how to have a good two-way exchange with her. You have probably already gotten a lot of great advice on this but the thread is rather long and I must admit I have read mostly just your posts and only a few of the other recommendations people have made. Setting the stage will help get her attention. But the actual conversation will probably require creating some real impact for her so she sees your perspective differently than she has up until this point. I think with some effort you can do this while you are leaning on The Leverage that she doesn't want to lose you or the marriage. It often takes a little bit of creativity and how you position things so someone can see it from your point of view. There have been a ton of good ideas written in these forums that you can take advantage of and if you are ready to have the dialogue we can write down some thinking about how to do it.