Get custody of your child. Also, I do not mean to be harsh, but you may want a DNA test to see if it is indeed your child. I would also get yourself tested for HIV. She may not be bouncing between you and just one man, and who knows the status of their health? It is time to move on brother, she won't stop making you a cuckold. You are only damaging yourself in this scenario. It is clear she has no real regard for you whatsoever. There are a lot of women out there who will not treat you this way. I realize you have a tremendous emotional investment. Who among us wouldn't? I am sorry for your loss, but it is just that, brother.
Jon, you're story really does touch the heart. The level of suffering of all three of you is epic. I believe you need to do what God tells you to do. But if you want to ask yourself - ask yourself this: Why did you marry her and no-one else in the first place? Maybe finding that out for yourself will put you in a place where you can move forward and feel less guilty or even victimized. It has been mentioned before and I agree that your daughter needs proper care and protection regardless of your relationship with your wife - once a kid is in the picture she really needs to be the first responsibility.