I'm confused - what's he been doing for the last 2 years? Did she take him back? Were they trying to reconcile? Did they divorce? If he was back or trying to get back with her, why did he continue to have sex with you? Once you found out he WAS still with his wife (BTW - separated is still married), why did you continue the affair with him?
Regardless of the answer, he needs to be active in his child's life, and I don't see how he can do that without his wife being aware of it. Since she's going to find out, it's probably a better idea to tell her. However, considering that she probably already hates your guts, you should not be the one to tell her. Her husband should be the one to break the news to her (and face the music when she blows up at him over his continued infidelity). Give him a deadline by which to do this. If he doesn't, have a third party break the news to her.
You also need to speak to a lawyer to make sure that you protect and secure the child support that this man owes to his child.
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