Hourour Musuko
https://www.mangago.zone/read-manga/hourou_musuko/
I haven't read it, but I have heard that it's really good.
I.S.
This work deals mainly with intersex people. I have just started reading it so I am not sure whether it contains trans charcters, but one of the first stories do show someone choosing to undergo gender-related surgery.
https://www.mangago.zone/read-manga/kanojo_ni_naritai_kimi_to_boku/ Her childhood friend is trans and the story is about the two of them
https://www.mangago.zone/read-manga/boys_run_the_riot/ Trans boy starts a fashion brand with the new transfer student at his school
https://www.mangago.zone/read-manga/yuureitou/ Main character and Trans guy are trynna solve some mystery, i haven’t read nor finished this so idk the plot after a certain chapter
https://www.mangago.zone/read-manga/hourou_musuko/ MC is a trans girl, about hoe she deals with gender growing up, it gets weird (?) at some points but it’s an overall good read
https://www.mangago.zone/read-manga/shimanami_tasogare/ Most of the cast in the manga is queer in some way. Iconic manga, Mc is gay.
I recommend going through the
LGBT tag: https://www.mangago.zone/tag/LGBT/
And the
Trans tag: https://www.mangago.zone/tag/Trans/
To find manga that has more positive/explicit rep that I assume u are looking for
Actually I think the https://www.mangago.zone/tag/transgender/ Tag might be better. Idk I skimmed them
Ive yet to see any trans rep on this website so lmk if their are any stories with trans main chars!!!