Cemetery Boys is a modern urban fantasy book with a trans man as the main character. It's post transition though, so it focuses less on dysphoria and more on transphobia. It does feature a gendered magic system though, if that's relevant to your interest. Plus the voice actor for the audiobook went on to voice Raine Whispers from the Owl House, so that's fun
Mmm, so in my experience gender dysphoria is rarely addressed in fiction. There's a bunch of reasons for this. Trans characters are relatively rare to begin with and it's easier to reveal that a character is trans if they've already transitioned which, ya know, helps deal with dysphoria.
The best example I can think of comes from the Whateley Universe. In particular the stories featuring Jade / Generator. The Whateley Universe is a superhero setting where it's relatively common for those who gain powers to also undergo physical changes. This includes X-men style mutants, but it's also used to explain the number of superheroes that end up looking more like male or female supermodels. As part of getting their powers their bodies become idealized. In rare cases these physical changes can include having your body swap sexes. Weeeeeell, I say rare cases, but the stories particularly focus on transformations and stuff like that so pretty much all the characters in the story end up like that. Jade is a rare exception in that she's a transgirl but doesn't get the magic sex change that most of the other main characters get. The dysphoria aspects with her can be relatively subtle at times, but there are moments such as being jealous at another girl getting her period because she physically can't. The stories are free to read and the Whateley Universe as a whole has a ton of content, but honestly the website could use a bit of an upgrade. =_= Whateley Universe
Next, is... Hmm... Well, I can't go into too much detail into this one without spoiling things. All I can say is that pay attention as you read it and you'll see the role dysphoria plays. O Human Star is a webcomic about someone who comes back to life under mysterious circumstances 16 years after their death and isn't handling it well. It's something that really needs to be read in it's entirety to be appreciated which can be a tall ask for when you're just looking for something for research, but I can't recommend it enough. It's an excellent story. Chapter 1, Title Page – O Human Star
Finally, and this is somewhat of a complicated one, is the case of Bridget from the fighting game Guilty Gear. Bridget is from a village with a superstition saying that twin boys were bad luck. Wanting to get around this her parents raised Bridget as a girl and her twin brother as a boy. Seeing how guilty her parents felt for doing this and feeling that the whole superstition was stupid she set out to prove the superstition was wrong by becoming a wealthy and famous bounty hunter. She succeeded! Now in her most recent appearance in Guilty Gear Strive she has to come to terms with the fact that despite not having the superstition hanging over her head and all the effort she put in so that she could be seen as a guy she... well, she still liked being a girl. Since it's a story from a fighting game you can probably find all you need on Youtube, but be warned that there's plenty of people that complained about her coming out as trans in Guilty Gear Strive by saying that it negates her previous story in the earlier games. This, I find, to be bullshit.