I'm confused if I actually beat the main-story or not.
I've kill the big, black, mean, evil dragon and had the Blades tell me to kill the dragon on the throat-of-the-world... Which I tried, but failed; he wouldn't die :/

That quest also disappeared for me too.. or I just can't find it in the mass amount of quests I have.
I also can't find the Blades again, I know their in the Sky Haven Temple, but I don't remember where that place is located. :/ (It's hard to find a specific location when I have hundreds)

Skyhaven is in the middle of the west side of the map, it has a shield shape. I think you could consider the dragon born quest line to be the main story arc, but it is really only the beginning and several of the other quest lines are just as epic. The quest for the elder scroll was my favorite.

I don't know about killing the traitor dragon, I chose not to, I believed his story and felt that the blades where being unreasonable; especially after I killed Alduin and saved the world they still want a complete dragon Holocaust. Anywho I really regret signing up my favorite followers as blades now.