TMB,
Sorry you find yourself here, but this place is full of people who have faced similar problems, and who can provide ideas about worked and did not work for them.
The first thing that strikes me in your post is that you really don't trust your gut on things. I think that you should. That inner voice was put there for a reason. That voice is YOU, TMB. When you don't listen to it, you become detached from your own emotions and can feel like a ship that has no rudder. You drift, you feel lost, when all the time there is that inner voice that is trying to help you. So please, as one positive consequence of all this, re-connect with your 'gut', your inner voice, and trust it. When you start trusting it, you will start trusting yourself. When you start trusting yourself, your confidence grows. It is a healthy thing to have working for you.
The second, and obvious, thing to say is that very few marriage counselors recommend affairs as a good way to improve the quality of a marriage. That decision is made by those who cheat, when they decide that rather than go into counselling, or talking, or making some effort themselves to improve things, it is easier to just fall onto, or under, someone else. Thereby making things much worse! So whether or not you made some mistakes in the marriage, it was your wife who chose to make none of the efforts described above, and instead to use the issues in the marriage as an excuse for cheating (which you say she has done several times before anyway). So please get rid of any notion that 'pushed her into the arms of another man' (as so many cheats like to say). Your wife made the decision to cheat (yet again), you didn't.
She revealed something terrible happened to her that she cannot talk about? That is very sad, and she needs therapy for that. But you know what? Loads of people have terrible things done to them, far more than we realise, but they do not see that as a license to abuse other people. Your wife's decision to bottle it up is 100% the wrong one, and she needs professional help with that. It will continue to mess up her life until she makes the decision to do something positive about it. But whatever demons she may suffer from, it is her choice to live with them, and they are not in any way a justification or a reason for cheating on you. Just like the issues in the marriage, very few counselors would recommend cheating as a way to fix childhood trauma. So please, by all means treat it as a sad thing, and a problem she has to fix, but do not let it be any kind of justification for cheating.
You question whether you 'rushed' the decision to move back into your own home after your wife cheated (again). TMB, I honestly don't think you should ever have left. For a start, you have absolutely no proof that your wife has ended the affair. With you gone during the week after the kids were in bed, do you really know what she was doing?
You say:
She's said to me many times, alone and in therapy, that she loves me but she just really dislikes me right now. That she doesn't want to be around me. She's said 20% of this is what I did or didn't do in the past, things I e said that hurt her ect...and the other 80% is how she feels about herself when she's around me, the shame the guilt the fact that she's not worthy of my love, that she's a terrible person. During this time I've also set out to correct all the issues she had told me about that may have opened us up to an affair. Since D-day I'll do anything around the house that needs to be done and take care of the boys. Before she comes home kids are all taken care of, fed, washed and in bed. Dishes are done, vacuuming is done, any laundry, any straightening up...anything that needs to be done so that when she gets home she can have her me time, self examination and time for introspective moments ect. Just want her to come home and relax, get her voice back and time to heal and get better. But the results in my eyes are she's getting more and more distant. If it was me that did this I'd be kissing her sweet ass for giving me another chance and doing anything I could to be next to her. Instead I feel like that's me. She's getting everything and more while I'm being ravaged by the twisting wind of emotions and lack of contact. She makes me feel like she wants nothing to do with me. I feel like I just don't get it.
I am saying this gently, but although she says she loves you, I think she is losing her respect for you. And that is why she says she dislikes you. She has behaved badly, more than once, and you are running around after her like a servant. Stop doing that. By all means help with the housework, doing it together can be something that brings you closer, but you should not be waiting on her hand and foot. It's like you are rewarding her for cheating. She probably cannot understand that, and may even wish that you would stand up for yourself more, and fight back on some things. Think about it: you see what you are doing as a manifestation of love (and I know it comes from a good place in you, you're a nice guy), but what effect is it having? Does she appreciate it? No. Because she may be starting to see you as someone that she can do bad things to, and you just let her do them. And you respond to her bad behaviour by acting like you are to blame, and trying to please her even more. She knows she's done wrong, but you aren't telling her that, you aren't defending yourself, and she is starting to see you as a kind-hearted human punchbag who permits her to do bad things, and whose loving response - rather than the usual one she might expect - leaves her feeling bad about herself and like all she keeps doing is hurting you. And instead of standing up for yourself, you let her do it again and again.
The point is, you have to have some boundaries about what you will, and will not, accept. If she feels like she can do anything to you, she will. And it becomes a cycle that will keep repeating itself, which it sounds like it already is.
There are various things that you can do, as other posters have suggested, but I really think that it would help you very much to get some individual counseling to rebuild your confidence, get you trusting your gut, and to establish some boundaries about what you will and will not accept. Once you have some confidence in you, maybe she will too. But first and foremost, do it for you.