Okay this is a bit harsh but considering the thread I guess it's okay to be a bit of a bitch.
Joe has already commented on the more technical stuff better than I could, so I'm just gonna write my more subjective criticism.
The story had such a strong vibe of being of being written by an outsider that it honestly made me uncomfortable.
more bulky than the average Japanese man.
The girl seated in front of Hideki was rather pudgy. By Japanese standards, she was actually quite large.
Did Hideki spend most of his life abroad? or is there some other reason Japanese standards aren't simply default standards to him?
Once Japanese language, math, English, and biology had passed
国語 translates to "national language" or just "language". Japanese language class is what I had at uni in Sweden.
He returned to his desk with a small pile of various things from the hallway vending machine; two rice balls, a variety of croquettes, and a couple of pieces of fruit.
Is this a science fiction story? Japanese vending machines are pretty great but they're not even close to that amazing.
At the corner of the school yard near the back gate, stood an old-fashioned Japanese building.
Japanese people does sometimes refer to things as 和風 which can be loosely translated into Japanese-style. Did you mean "old-fashioned Japanese-style building"? That's superfluous, if you want to add information, add actual information such as, is it Edo-period? Showa-period?. Or did you just need to remind us that the building is in Japan and so Japanese desuu? We already know the building is in Japan.
They dialogue have a real uncanny feeling. I guess I can be nice and say it creates an atmosphere.
Over-all the writing is okay for a hobby-writer, but it's for very good reason writers advice against setting stories in real-life countries you haven't lived in. At the very least read some books by Japanese authors.
Also are you LGBT and have lived in Japan and talked to actual gay and trans people there? If not kindly f*** o** and do your research instead of grossly generalising people you don't know. Sorry but ppl constantly exaggerating and spreading misinformation about LGBT in different countries, whether is overly positive or negative, pisses me off!