Is the prayer valid if the congregant, during the Fajr prayer, only recites the qunut supplication: "O Allah, guide me among those whom You have guided, and grant me well-being among those whom You have granted well-being"?

If the Imam performs Qunut in the Fajr prayer, the congregant should follow him in the Qunut. If he hears the Imam's Qunut, he should say "Ameen" to it. If he does not hear it, he should make supplication silently. In all cases, his prayer is valid.