I don't think based on what you have posted that you can and will deny that your wife has been unhappy for awhile. For her to figure why she was unhappy IMO is going to take longer then 3 months.
Look I agree with you that your situation is a little different then most situations in that it's not because you got fat and lazy or because your a wimpy beta. I think it is more because she didn't feel loved and wasn't get her needs met.
Your situation is a lot like mine. We had sex right up to the week she left and I am talking about all kinds. The main reason why was for the last 10-12 months I never once tried to change her mind or asked her to reconsider. I realized that if we were ever going to be in a relationship again it would be because it was her idea and she had to make amends for all the pain she caused everyone.
If you engage in a relationship with her again it should only be under the conditions that:
1) She sees you as someone of extremely high value 2) She views a relationship with you as something much better than a life with someone else or a life alone 3) She's willing to work to win you
Without those three things, she's going to walk again down the line, because she really doesn't have the motivation to work with you to change anything, your relationship will keep seeking the same equilibrium it has had because of how your personalities and issues come together.
