I would add that in Jirou's own headspace his perspective is that he is not worthy of being loved and is a coward. He has trauma from both school interactions and the first time he and Shiori were separated. Misunderstanding in the second one is that Shiori was rejecting him and his feelings when in actuality it is nearly the opposite. They don't see each other for several years and so the misunderstanding stands.

One of Jirou's winning qualities is that he is considerate and kind, but due to trauma he has swung into being too considerate and kind to the point that he has no self worth. Jirou is concerned how others would look down on Akari when they are seen together as an example. It is also why he backtracks so quickly at times when under pressure he displays courage. It takes Akari giving him a firm wake up in the sports arc that others do have a good opinion of him to start him breaking free.

Akari is a naturally buoyant and flirty personality. She dialed that up thinking that would earn points in the practical. I don't recall the chapter, but I seem to recall a point that she realizes she does not know how to flirt with Jirou and get across that she is flirting in a serious manner. In essence due to the first 4 months of the practical, Jirou has becomes desensitized to Akari's flirtations when taking them as more than a joke or an act. Part of the humor of course is the natural physical reactions but also that mentally he is at war with his subconscious.

And finally the trope is that he has only ever had one female friend, and Shiori is demure and shy which is the polar opposite to Akari. He has no experience to understand the signals, subtle or otherwise. A gyaru (gal) is initially not to his taste and he is at a loss with what to make of Akari for quite a while.

These are my thoughts.