Hey Tyler,
I totally understand. I went to an all girls Catholic Highs School for 3 out of 4 years. I never fit in either, but didn't understand why until much later when I finally realized I'm a transguy.
However, I did find a way to get a little relief. While I was a loner, I was also pretty non-femme/butch. I"m not lesbian. I like guys (which made the whole all-girls school thing even lonelier, as there was a strong underground lesbian contingent there, but I wasn't part of it.)---which also meant I pretended femme some times so I could date. I guess I'm just now realizing that I did a lot of back an forth on the masculine/feminine scale trying to make myself socially fit, although I never did. I wish I had known myself enough and been aware enough to be okay with myself. I'm really glad you know who you are.
So maybe if you work on coming off as a masculine girl, with emphasis on masculine and just putting up with the girl part because you have to, maybe that will help some. Also, I stayed as invisible as possible. I did my work, didn't get into trouble and didn't make a lot of waves even though I wanted to.
Good luck! High school is tough, even for people who aren't trans*. Just keep breathing through it. We need strong transguys like you in the world!