What are examples of the gloomy atmosphere Joyce tries to create that gives the sense of struggle? What is the significance of the three book titles that belonged to the former house resident, a priest? What is an example of the pervasive theme of "light vs. dark" that is symbolic of religious good and evil?

The priest left the following books on the shelf: The Abbot (by Walter Scott), The Devout Communicant, and The Memoirs of Vidocq. The first book is about Mary Queen of Scots and blends Romanticism and sexuality with political conflict. It is a sequel. The third is a crime novel about a French police commissioner who is also a thief. There's more than one book with the title The Devout Communicant. Any of these would focus on Christian religious devotion. Taken together, they communicate the idea of coming in on an ongoing story, getting a new perspective on things you think you know, that religion is important, but also that you can expect figures of power to have secrets and a secondary identity.
Taken together, those books contribute to the gloomy atmosphere in the story. To identify more specific examples tied to the youths, look at lines like the very first: "North Richmond Street, being blind, was a quiet street except at the hour when the Christian Brothers' School set the boys free." The boys aren't off school. They are free, meaning they were contained or trapped while in school. They go to school in a "blind" street." Right away, that's pretty bleak.
As for the relationship between light and dark, see the start of the third paragraph: "When the short days of winter came, dusk fell before we had well eaten our dinners. When we met in the street the houses had grown sombre. The space of sky above us was the color of ever-changing violet and towards it the lamps of the street lifted their feeble lanterns."
They eat in the dark. They meet in the serious dark (as indicated by the sombre houses.) They sky is violet, which is quite dark, and the lamps are too weak to light anything. This is less good and evil than hope and despair—the gloom mentioned before.