Section 31 is definitely mentioned, but it's a throwaway mention about "Harrison" and is a fabrication (as I understood it). Didn't hear 'augments' ever mentioned that I remember.
Alice Eve is screaming because Khan kills her dad (Peter Weller) in front of her by squeezing his head with his hands.
WarpFactorZ is right on the money with the rest, other than the fact Uhura helps Spock out as well.
Not sure about that screenshot. It could be. They run pretty far before they get on the barges, and the Vengeance does come to a stop in a position like that... but it could just be a building.
The score was one of the best parts, particularly if you liked ST09's score.