She needs to fucking say it directly to him. All of his self doubting has been directly caused by either her actions or words. It's starts with him being in MS while she was in HS and he
overheard her telling his sister that he was like a little brother (repeated
here). She also does things like trying to make him feel flustered by having him do her underwear, which instead make him believe she doesn't see him as a man (same
page). She kissed his cheek and
denied it meant anything. Along with that she
vehemently denies to his sister that she asked him on the aquarium date right in front of him.
She has no one to blame but herself for being coy and constantly pushing him away.
I get what you mean, but I can't fully agree with your examples, two of them come from the first chapter, which obviously is going to have some points that make the MC doubt that she has romantic feelings, also one of them is a flashback to two years before the story (feelings can change you know), same thing with the repeat of that flashback. And the other two just look like she is getting flustered, it's not like she is really teasing him on purpose in these ones.
I get that she needs to go on the offensive more (and more importantly since she is doing that already, stand by what she is doing), but I just don't think making her think she might actually be misunderstanding his affection is a good way to go about that, at least not at the point where we are now.
All in all, obviously I think both of them should just be honest about their emotions, but like that's pretty much what this story was from the beginning, so I am not going to fault either one of them for not reaching that point yet.