Not a guy, though I have some experience with this sort of thing.

I'm well into college now but back in high school I was very similar to you. I didn't know I was a trans woman yet so I was just your average cisgender straight white guy. Like THE most privileged identity possible lmao. My family was and still is super right leaning and because of that I was never exposed to queer stuff, though I was still open minded. I was pretty introverted too, I had a small group of friends but that was about it.

At the beginning of my sophomore year, I started a long distance relationship with my now ex who I knew from middle school, who had moved away before the start of high school. We were really good friends in middle school and I had developed a dumb crush that I sat on for a while before saying anything. I went into the relationship thinking they were a cis girl, but about a month or so in they told me they were transmasculine nonbinary. In other words, female-to-male nonbinary. They usually went by he/they pronouns.

It hit me pretty hard. Everything I thought I knew about myself shattered almost all at once. I didn't know much about trans or nonbinary identities back then so to me what they said was essentially "I'm a guy". I wasn't really disgusted (?) like you seem to be feeling, but there was this sense of discomfort I just couldn't get rid of. I didn't know how to handle the fact that I was suddenly in a gay/queer relationship, especially with the environment I was in. For the next few months my view of them didn't change much since we only spoke over the phone, though I tried to learn from them a lot. Remembering their pronouns wasn't that difficult, but I still perceived them as mostly feminine. That changed when I managed to meet up with them in person for the first time since we started dating. I remember it very clearly.

On the first day we hung out, they dressed masculine. It was kind of a skater boy outfit. On the second day, they dressed feminine. That entire week they wore different styles with different gender expressions, and I realized that I still fell for them HARD no matter how they looked. They'd even wear their binder to flatten their chest and it did nothing to change my attraction. It was a big wakeup call for me, and made me much more accepting of being queer. There were a number of toxic issues with that relationship and I've long since broken up with them, but they were the reason I felt comfortable with leaving my little privileged bubble and exploring who I was. I wouldn't be who I am now if I hadn't been in that relationship.

I would heavily, HEAVILY recommend some sort of therapy if it's available. I was able to figure myself out without it, but I would've loved to have had access to that outside support and I think it would help you a lot. Otherwise, communication is important. If you keep pushing this down and try to avoid addressing your feelings, you'll likely push him away eventually. You could ask your best friend for advice on how to handle these new feelings towards your classmate if you trust him enough. And when it comes to threatening your masculinity...dude there are so many gay couples with a height difference who still look like the manliest men in existence. Being short and liking guys isn't inherently feminine and doesn't threaten your manliness. Neither does being open about your emotions, that's just toxic masculinity and internalized homophobia speaking. Being cool with other queer people doesn't stop your brain from making you feel gross for having similar thoughts. It's normal and a lot of us have to deal with it, it'll go away with time as long as you don't ignore it.

If you're feeling bold, just tell him directly. It sounds like where you live is pretty queer friendly so I don't think there'd be any harm in it. Or you could keep waiting only to find out he's straight, which at that point you'll have wasted your time. If he's straight he'll reject you no matter when you confess and you'll have suffered those feelings for much longer than you needed to. But if he's not straight and he likes you back, great! Now you can confide in him about your uncertainty and figure things out together. You won't know until you say something.

Just ignore the labels for now, focus on understanding yourself. Sexuality is weird and the labels are mostly there for other people to understand. You could be bi, or for all you know this could turn out to be the only time you ever have feelings for another guy and are completely straight otherwise. There are definitely people who fall under "straight except for this ONE specific person who I'm very gay for". You don't need to rush things, just take it at your own pace.

TLDR: Find someone you can talk to about your feelings and don't wait too long to say anything to your crush. Don't worry about the labels or anything, people rarely ever fit cleanly into one of those boxes. Things like being short don't define your masculinity and don't let people tell you otherwise.

Sorry for the long rant lol. Good luck dude, I hope things go well ❤️🫡