Hi evilfish,
When it comes to working out your gender identity, you're really the person who can determine what one(s) feel right to you. If you haven't already done so, this piece goes into some indicators that you might be experiencing gender dysphoria:
Trans Summer School: So I Think I Might Be Trans. Now What?. Do any of the things described feel like they apply to you?
Too, it does sound like this might be about your feelings about vaginas in general rather than just your own (if I'm misunderstanding that, please correct me). You mention they freak you out and feel complicated; can you tell me a bit more about those feelings? Do you have any sense of where they came from? Are there particular things that feel confusing to you about them?
Since it sounds like you feel that your vagina doesn't look "right," I want to give you this piece, which does a really good job explaining that genitals, including vaginas/vulvas, are way more diverse in how they look than some people think:
Vagzilla! (Or, All Genitals Great and Small)