(which we know Scotty can do, because he sets it to kill (red barrel) when he gets his phaser)
There was some line when they first boarded that the phasers can only be only set to stun. "There's won't be," Khan says.
What I can't figure out was the techno-babble line that prevented the Vengeance from firing on the Enterprise. Khan ends his explanation by saying "Which gives us the advantage."
But his explanation didn't make a lick of sense.
Another thing I can't figure out was whether Khan acknowledged Sulu's deadline in any way.