"took in" is another way of saying "looked at it" but it also has a contemplative feeling to it.

"I looked at the wall", doesn't invoke any feeling.

"I took in the painting on the wall", means not only did you see it but you thought about what you were seeing.

"I looked at the painting on the wall and took it in". This is another way of saying the same thing.

You "take something in" when you look at it and start to think, or you start to have an emotional reaction.

Elizabeth looked at, and "took in" the rafters and the char (char is that black burnt wood, or perhaps in this case it is wood that has been blackened by the smoke of candles over many centuries) and the fixtures hung like iron crowns. "Fixtures hung like iron crowns" is a simile, or a comparison between the actual object and some different object. The fixtures means chandeliers. He describes them as "iron crowns" so I imagine very old iron chandeliers which are hung from the ceiling with a chain, and on the chandelier are many candles. That looks a bit like an iron crown, don't you think? It's a very nice simile.