Man that is hard. You have done such a good thing by adopting him but it looks as though this journey could take you in many different directions not just because the uncertainty of the father but the two that are suspected of being it have such mental illnesses that could effect him later down the road.
I can not even begin to imagine what you are going through but I think the best thing to do is be honest. Sit him down and talk to him about what you know. You need to be truthful as he is 15 and he should know even though that could hurt him.
Does the man on the birth certificate know anything further or more concrete about the possible identity of the dad, that could help to shed some light on the possibility of the young woman being your son's cousin? (Does he even know for sure that he cannot possibly be the dad, or did they just think it?)
Frankly, if the boy is only 15, it does not sound like he is planning on marrying the girl and raising a family. Romance changes fast at 15. I'd just focus on being sure he is dead accurate with birth control.
This jumble over his paternity is probably something he needs to know sooner or later, but hitting him with a list of possible candidates that are all bad will not help him at age 15. If you wanted to explore the issue privately, you could first rule out for sure the guy on the birth certificate. I think this can be done with DNA testing, though I don't know how it's done without the mom. Then one by one, it might be not so bad to start ruling out the other possible guys the same way. If you don't want to go through all of this, it might be something for the young man to do himself, once he is of age. But I would not hit him with all of this right now. 15 is not a great year for a lot of kids, and this would be the mother of all revelations to put onto him atop hormones and teenage angst.
Focus on making a great home life for him. By the time he does know the tangled mess, he might not care so much because you were always there for him and had his back.