AFWAW, Your commander sounds like a good man who has your best interest.
I would not recommend that you talk to your wife about the divorce...I would not tell her you talked to your CC. Nothing has changed. If you thought the fear of getting in trouble would stop the affair and she would consider MC for the two of you I would say do it but that is a judgement call for you to make. Nothing you have told us makes me think she will stop until Oct and then on to another OM. I think if you tell her they will just be forewarned and make it harder to find out who he is.
Your goal should still be exposure...the name your daughter has from the computer game is a good start...send your CC an email with his name and tell him you are not sure if this is the OM but he was on her computer...he can have PERSCO give him a duty section for him. I say this if your goal is to try and save the marriage...until the affair is over your wife will continue as she has.
On the other side...if she is willing to give you everything in the divorce to include primary custody you should consider filing...the proof will (as Puppy said) help you with custody...do you think she will fight you having custody? Have you talked to your daughter? What does she want?
For now it is best you investigate and stay calm. Get your legal issues fixed as best you can to include personal property.