eh, I went back and read your more detailed situation. it's possible that she is not in an affair right now. It's probable that she WAS in one, and is now in recovery from it.
the question is, is she going to transition from "having an affair, to being single", or from "having an affair, to being married again" ?
In my opinion, you should show her that you can be there for her, in the way that she needs you to be. That would be: in the house, silently, maybe taking care of little things without asking, staying out of her way, and without talking about your relationship, unless she starts it.
This requires you to put yourself aside, and think of her, continuously, for weeks.
if you dont think you could do that right now... then you need to work on yourself to get to that point. Because that's what marriage calls for: being able to set yourself aside for a time, for the benefit of the other person. If you cant do it, then you arent ready for a recovery of your marriage yet, so merely "being apart" is not going to improve things.
Do you agree with that?
My current status: june 2006. Wife ran out and filed D. Finalized Jan 11, 2010, after 12.5 years M. 3 wonderful sons caught in the middle