~~I Wanna Be Your Girl comes to mind, although I have to admit it's still in my to-read list, so I can't personally vouch for its quality.~~
EDIT:
spoiler for this manga but it’ll save you some disappointment
Sadly, I’ve learned that this isn’t yuri; the trans girl ends up being straight for some guy. So not the representation I, a transbian, was hoping for.
Wild that your list is bookended by movies I still need to watch. Tokyo Godfathers is a yearly holiday rewatch for my partner and I, though, and Perfect Blue is excellent, of course.