First and foremost, this is a terrible situation and I'm truly sorry that she has placed you in this mess.
Secondly, while you may not be able to understand it, it is entirely possible that she may be a lesbian, or at the least, bisexual. She might have been using you as a beard or something. Are her parents homophobic, by any chance? That may explain why she has been trying to act hetero when she is truly homo.
Third, you need to know that THIS IS NOT YOUR FAULT. Your wife made the choice, not just to cheat, but to disrupt her child's life by getting rid of the man this child calls Daddy and moving some random woman in. All of those fights and excuses that she is giving about the state of your relationship is her desperate way of trying to get rid of you. As painful as this is to accept, she does not want to be with you anymore, and the best course of action is to file the papers. However, the big issue here isn't your wife. It's your child. I'm not a lawyer, but if you have simply been raising this child and have not legally adopted her, you'll have no claim on her. The courts are big on biological families, and if you guys split, I fear you will never see that child again, which is unfair to both you and the child.