Only one fic springs to mind when it comes to transgender which is
The Many Faces of Harry Potter in which Harry has multiple personality disorder and when differant personalities emerge his body changes to match and several are girls. Harry, the main personality realises he wants to be a girl and so forces his body to change which is much harder than the other changes. Cant member much else about the story but it's pretty good and original and the author also has MPD so they know what they are writing about. I dont think she has anything to do with snape. Ther are a few stories in which Harry is changed into a girl and accepts it easily and it's suggested he was transgendered but it's only a very brief mention.
Edit:
I did a search and found
Holly which seems to fit all your criteria, a quick scan shows transgendered, with snape and Ron gets expelled. If it's not this one then I'll have another look.