What are some metaphors in chapters 1-3?
The first metaphor I see is where Holmes says to Watson
It may be that you are not yourself luminous, but you are a conductor of light.
Holmes does not, of course, mean that Watson carries light around with him or that light can go through him. He is using light as a metaphor for wisdom or insight and is saying that Watson has no insight but helps others to get it.
Towards the end of Chapter 1, Mortimer says that he is
A dabbler in science, Mr. Holmes, a picker up of shells on the shores of the great unknown ocean.
Of course, he does not mean that he literally goes and picks up shells near an unknown ocean. Here he is using shells as a metaphor for knowledge and is saying that he gets little bits of knowledge but does not really touch the main body of the knowledge (the ocean).