There is actually very little metaphor in the above:
as the shades of knowledge deepened, the shift in emotion
This is hard to say for sure, but probably not a metaphor. The writer is describing his/her interpretation of the changes in the person's facial expression, and this is direct observation.
the flare of relief, the flush of embarrassment that came with the realization she had mistaken the purpose to my last visit
In this case actual changes of facial coloration are being observed. In particular, most people are familiar with seeing people whose faces turn red with embarrassment, and "flare of relief" suggests a change in expression and color that could be associated (by the skilled observer of human behavior) with that emotion.
Agnes's journey mapped in colours and jewels
This is missing critical context. As I said in a comment, if "they" are staring at an actual map with actual colors and jewels identifying where Agnes has traveled then it's a simple literal description. If the context is something else then there could be a metaphor.
my mouth was so dry it was glued shut
This again is a literal description of the situation. At most it was hyperbole, but I have experienced situations where the "glued shut" description fit pretty literally.