The protagonist has difficulty with his emotions and social coping mechanisms, and is being bullied by a secondary character. I'd like to dissect the emotions and reactions in him as he learns that a confrontation is inevitable. Are there any published works I could read which does a good job of this already?
Yes; see Worm which is a Web Serial. The initial arc deals with bullying of a 15-year-old girl by her classmates, and I found it haunting.
Other good examples, which come from books (so, not readily available), include Tangerine by Edward Bloor, and Speak by Laurie Halse Anderson. In the first book many of the worst bullies in the Main Character's life are members of his family. In the second the Main Character spends the school year attempt to recover from rape and avoiding the rapist. It's a matter of degree and characterization for how your character deals with trauma.