AFWAW, My fingers are crossed...you are doing well. Do not think the OM is out of the picture yet. Why would he be? Your wife still has an apartment that he is free to visit whenever he wants. Do not get caught up in her guilt making you think it was your fault she did not rush home to you. if she wanted to she would have for no other reason than your daughter...I am sorry but something is still going on even if it is her just hoping he (OM) will call/visit/divorce etc. Again, you need to expose (with proof), end the affair, and work on your relationship. Great if she comes back (if affair is over, if they are still "buds" and talking/working out it is not over), regardless of the reason, at least that way you will always know you tried your best for yourself and your daughter.
You are correct about this is situational and honesty is best.
What was so bad in your opinion and your W about your marriage before Iraq? Everyone has low points...anyone so naive to think that marriage is not work has not been married for very long. The military makes it more difulcult at times due to long duty hours and deployments but the deployment is not the root cause...many more make it and become stronger because of the seperation...grateful for what we have thought.
Do you go to church? Did you talk to the chaplin? Did your wife participate in Heart's Apart while you were gone? I think not...
Do not get caught up in the revenge mode...it will eat you up inside and again, PT, self improvement, no alcohol.