Nitori is a lesbian and Takatsuki is straight
She's only ever shown interest in girls. She sees Takatsuki as a boy, but it's very debatable that she mistook her feelings for love when it wasn't actual attraction. The manga does like showing different shades of stuff, so I wouldn't think twice about it having one gay Transsexual and one straight one (Yuki for straight, and maybe Takatsuki unless he's gay or bi). Speaking of Takatsuki, it's even more debatable with him since he hasn't really appeared to like anyone so far. He did seem to like Yuki at first, though that may be a case of "I passed?" rather then him liking the fact a lady hit on him. He apparently could have liked his male middle school teacher, but that appears to be confusion rather then a real crush. Nitori and Takatsuki will trade first names
It's been lampshaded several times, and discussed several times. It doesn't seem they've taken much thought into name changes, and there's really few ways to make "Shuuichi" into a girls name ("Yoshino" can change into various things though). Saorin is going to do something to make Takatsuki uncomfortable again, and accidentally push him towards medically transitioning.
We saw that when she told Takatsuki that she liked his hair long, and that boys could have long hair too, he grew it out because it made him feel validated as a man. When Yama-p confessed his love, Saorin said that Takatsuki was a normal girl, and that the way he was he was very pretty and it would only get worse, which pissed off Takatsuki so much that he cut his hair off again to avoid people thinking of him as a girl anymore. Saorin is probably going to say something like "You're a pretty girl/You won't grow more/You're getting even more feminine everyday." This will trigger an alarm that makes Takatsuki act. Mako-chan will be the first of the three teenage trans people to medically/socially transition.
Given the events of Chapter 113, there's good reason (namely a supportive mother and, probably, father) to believe Mako will have the support needed to be more open about herself. This will probably also cause a ridiculous number of problems (the all-boys high school, for one), but it will be a clarion call to Shuuichi if not both Nitori and Takatsuki. Takatsuki will rediscovers his identity in college.
The fact that he reconsiders his transgender identity in high school seems less like he was genuinely believing that he might truly be female and more that he couldn't take the pressure of transitioning due to Chiba's comments of him wasting his feminine side. In college he will reconsider his gender identity and realize that his detransition was because of societal pressures and not how he actually felt.Chiba fell out of love/obsession with Nitori and into love/obsession with Takatsuki midway through middle school.
Around the time Takatsuki and Chiba make up, Chiba seemingly accepts that Nitori will never return her feelings and says she no longer loves her. This is also when Chiba starts suggesting Takatsuki should grow out their hair, repeatedly tells them how cute they are, and subtly and then bluntly pushes them to dress more femininely, even lending Takatsuki clothes and seeming upset when they returned them, all actions similar to how Chiba treated Nitori in elementary and early middle school. Chiba also shows signs of jealousy over and possessiveness toward Takatsuki: she pushes Takatsuki to go to the same high school as her so they won't be separated and seemingly isolates the two of them there until they're Mistaken For Dating, worries about Takatsuki abandoning her when their modeling photo comes out, and tells Nitori, Yuki, and Mako that Takatsuki is no longer thinking about transitioning before Takatsuki is themselves shown considering that, possibly to further the distance between the friends. When Takatsuki admits that they are more hurt by the loss of their bond with Nitori than the romantic rejection in chapter 121, Chiba thinks to herself that she wishes Takatsuki wouldn't say such sad things because she had always been so jealous of Nitori's and Takatsuki's bond, but she doesn't specify who she was jealous of, suggesting it may very well be both of them. Chiba does agree to go out with Fumiya around this time, but her reaction comes off more like she agreed because she was tired of him asking than her genuinely liking him, and she still spends far more time with and energy on Takatsuki than Fumiya after they begin 'dating'. Takatsuki is nonbinary
After spending their entire childhood rejecting being a girl, it really doesn't make sense for them to identify as a girl by the end of the story. However, there is the possibility that they are nonbinary, and potentially transmasculine, but not a trans guy. The kids in the series are shown to have rather poor understanding of LGBT identities outside of their personal experiences, so it may be the case that, when Takatsuki realized they weren't a boy, they immediately identified as a girl, not knowing that they had others options. After the events of the series, with access to better resources, he would discover nonbinary identities and begin identifying as such.