Well, you got through BD. It's a shame it wasn't on your terms, but it is what it is now, so you'll deal with it and learn.
I may be all over the place here as I'm taking time out from work to post to you (so forgive what may be a disjointed post).
What are the rules in Michigan with regards to one spouse being unfaithful? In my state, it can cost the unfaithful spouse money and custody rights (in some instances) and is never looked upon favorably if it can be proven. I ask because it may be part of the reason that your wife is denying an ongoing affair. It may, in fact, be over, but I doubt it. To Starsky's point- take nothing she says as the real truth.
I heard the same stuff from my wife - "I appreciate all the changes you've made, BUT......". It sounds to me as if your wife was waiting for you to dump her, but became impatient when you didn't and decided to beat you to it. Many WAS want the LBS to look like the bad guy that broke up the marriage. It helps them save face later. My wife flat out told me that she had been trying for months to get me to dump her by making herself impossible to live with.
At this point I agree with Starsky's plan - just remain polite and aloof. I would continue your changes, but don't expect to get credit for your actions. You're just showing her that you really have changed, and that you ARE this new person. Avoid pursuing at all costs.
The fact that your wife pulled the trigger for D even after noticing your changes does not mesh with her affair having ended. Why would she leave someone that was meeting her needs if she had nobody else? It doesn't make sense. You have a home and two children together. If there were no one else in her life that she was trying to free up time (and eliminate guilt) to see, then she would have given your marriage a year to sort out.
I would investigate and find out the truth about her affair. You can't have her living there and cake eating right in front of you. You must have boundaries.
Do not continue to argue with her. Funny thing about human nature- even when we know we are wrong, we will argue ever stronger against someone we dislike just so they don't win. In other words, whenever you go to tell your wife you will be ok, or that she can love you again, or the OM is no good for her, she will dig in even harder to prove you wrong. Just lead through your actions.