Episode 9/Chapter 23 reveals that Nanako became the Shrinking Violet because she was relentlessly bullied for her reliance on writing her words down. Had it not have been for Eiji, she may as well have found herself deeply under the Despair Event Horizon.
In episode 11/Chapter 41, Nanako began to cry as she thought she was going to miss out on the fireworks display with Eiji.
In A Lightless Christmas 4-Parter (Chapters 101-104) reveals that Nanako was bullied by a girl named Akari, who bullied her throughout elementary and middle school, who openly admits she enjoyed doing it. Amane and Eiji were worried when she didn't show up for club activity, and in 103, Eiji reminisces the time both him and Nanako exchanged senryu together, but notices a bent tanzaku board with nothing on it. Eiji and Komachi immediately notices this and Komachi tells Eiji to go to her. All the while giving him the scarf by unwrapping it and holding the torn wrapper with the heart tag torn in half. This speaks volumes of her relationship with Eiji.
Koto's dedication chapters. After she graduates, her thoughts were about Eiji, and she comes into terms that her feelings will never reach him, as he treats their relationship as Like Brother and Sister. She gives him a hug to indefinitely signify that she wants him to be happy with Nanako. For now.
Chapter 149. Dear God... Komachi is finally face to face with Eiji, and tries to confessed to him. But Eiji remembered Komachi from middle school (he's not aware they're the same person). When she asks why he didn't change his appearance, he tells her he considered but he feels like he's lying to them because even if they were close, it would eventually put a distance between them, and it makes Komachi realize that Eiji is the kind of person who likes someone for who they are, not who they're trying to be. The overall message hits home when the manga is saying "Be Yourself".
The tearjerker is compounded by an Imagine Spot where Komachi had the courage to talk to Eiji in middle school and they became friends through manga. When Komachi abandons her delinquent persona in Chapter 150, the first conversation she has with Eiji - asking him to be friends, and Eiji asking for manga recommendations - plays out exactly like the Imagine Spot. It would have been that easy.
There's a bittersweet moment in Chapter 162 when Tao and Kino arrive in the Literature Club to find it empty. They reflect that the club has been meeting less often since Amane has exams (and will graduate at the end of the year) and Nanako and Eiji underwent a Relationship Upgrade; Tao realizes that the Lit Club became a constant in their lives even as she realizes that sooner or later, their time together will end. Just to rub it in, the chapter title is "Change is the way of the world"."
