So I can get a list of friends via https://developers.facebook.com/docs/graph-api/reference/v2.0/user/friends and a list of friends lists via https://developers.facebook.com/docs/graph-api/reference/v2.0/user/friendlists.
Is there any way to determine if a friend is in a certain list or to get all friends in a list?
No. According to the API v2.0 changelog: "The permission read_friendlists no longer allows you to read the list of friends in a friendlist, but only lets you access the name of the list. This is useful for people building custom audience selectors when posting stories."