I'm not sure what to do. I can't stand being in this situation.
You were too hasty filing for D. You're only 12 weeks into your sitch, your emotions are running the show. It takes time, but you need to get past the emotions and start thinking more clearly before doing anything rash like filing for D. D is not going to bring you the relief and peace you hope it does.
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But I prefer to try and work things out with my wife. But I see effort from her. And now I wonder if I still want to be with her. Married 12 years, three kids 11, 9, 8.
Have you read DR? If not then do so right away, especially the chapter on infidelity. Many, many marriages recover from an affair, it doesn't have to be a deal-killer. An affair is usually a symptom of marital problems, not the cause of it. I'm not making light of what she has done, just saying you have your own issues you need to own and work on before you throw your M under the bus.