I like them the way they are. ;-)

For the first one, Shiraishi is eating fish on the bone, so she is quite literally lifting some of the flesh off it, leaving the bones behind. (This is part of a traditional Japanese breakfast. Like the traditional English breakfast, it is rarely seen outside hotels and the like these days.) She doesn't eat it until after the rest of the conversation has finished and we've cut away at the end of the scene; she doesn't have time. So your mental image is, in fact, correct.

Akira isn't surprised because he's forgotten the event. He's surprised because he hadn't really appreciated what it meant. It was a ceremony to stop the problems; he hadn't fully appreciated that the basic intent was that his father would "live" in the shrine.

For the last one, I wanted to emphasise the active aspect of enshrinement, hence the use of the verb, but "shrine where his father was enshrined" really sounds awkward. We don't really have good English vocabulary for this, because we don't really do it in England or the US.