The whomping willow was moved in the third film along with Hagrid's hut. Due to the location and the fact it is supposed to connect to the great hall it could be the clock tower. I doubt they'll do that, but that would take a lot of parts out of the car and tree.
I still think it will look like the one at Universal. Great Hall, Staircase Tower, Tower with stone bridge, Viaduct and the entrance, and the Astronomy Tower. Obviously, the great hall will be separate.
I think Hogwarts express, Diagon Alley, Hogsmeade, and ministry of magic would be the next D2C sets. Hogsmeade would go great with Hogwarts, just like Universal Studios.
I bet the great hall set will include the moving staircase tower as well. I don't think it makes sense to just do the great hall because they know more people will want the whole castle.