Yeah, the bunker having lots of useful literature makes perfect sense, and her leaving the books behind does too. After all, having spent almost 20 years just reading them, she's bound to know them by heart.
A couple of generations, putting her to around "our" Y90 would work if the shelter either had gi-nor-mous food stores, or (this probably makes more sense) had a small protected area, let's say electric fence with solar panels, inside which they could grow food, and they kept the preserved foods for safe keeping. The fight could have erupted around whether to open the by now nearly sacred stores or keep preserving them. Being able to harvest some fresh foods from this area (even after the fence fell into disrepair when there were no adults to do maintenance) would also make sense as she was a small child and would need vitamins and nutrients to grow into a strong young adult. Canned foods can stay more or less edible for decades, but the vitamin contents won't. Furthermore it seems more plausible that the people would have survived if they had some land area to get fresh air and sun too.
As for the religion, I don't really want to suggest anything as I'm not Catholic nor do I know the practices very well, and I might end up saying something offensive. If you like the idea, just think about something, anything really, that a child could misunderstand and after mulling it over and over and over again would come to their own conclusions.
But, especially with the assumption that spiritual presences are real in this world and she may actually have a real and present guardian angel, I also think it would be believable for her to have had access to religious books and with the help from those and supported by the angel (even if she can't really detect its presence) she could have gotten it right. If she was left to her own devices with only a Bible and memories of a five year old child, she could come up with anything whatsoever.