So I killed Mr. House and replaced him with Yes Man and I got to know the tribes I should get to know. But I can't progress forwards. I mentioned every tribe except for the Great Khans (Convinced them to suicide bomb) because there is no option to mention the Great Khans to him, meaning that I can't tell him that I got to know every quest, preventing me from finishing the game with the Yes Man.

Ouch, I don't know. Maybe you could try reloading a part of the game. Or maybe you didn't kill everyone in Red Rock? I'm not sure.