Hey there. I can't remember if I came out to my guidance counselor or not, but I told some other teachers in high school. In college I had to disclose multiple times, so I can give you some advice based on those experiences.
After talking to her about your Spanish class, tell her you'd like to talk about something more personal. If the door isn't already shut, ask if you can shut it. Not only does this give you privacy, but I've noticed I was taken more seriously when I offered to do this.
As for what to say next...You can ask whether she has any experience with LGBT issues. If yes, you can say "I'm transgender" or however you want to say it. If she says no, you can ask "Do you know what transgender means?" From there, talk about what that means for you. For example, a couple years ago I told my dorm supervisor that I was transgender, meaning that I was born with a female body but mentally I am male. After that, we talked about dorm arrangements, roommates, and privacy.
So after explaining what being transgender (or however you explain your situation) means for you, segue into the restroom and gym situation. Bring up pronouns and coming out when it feels right in the conversation.
I'm not sure what questions she might ask. Probably something about your parents because you're still in high school. I can elaborate on any of this if you want. I just don't want to overwhelm you with a huge wall of text.