Um, wait a second. The girl with the slingshot is Alex. Danny was calling her Ali for short. And I believe her boyfriend is Karl, the guy who was in the cage before Kate. And why would they have killed Jacob if they were paying attention to Jacob's list. If this list mattered so much, wouldn't Jacob's life be a bit more important. I think you are a bit confused.

Oh, and they said Shepherd wasn't on Jacob's list. (so, Jack) Which makes me think that Ben added him so that he could do the surgery.