I actually began transitioning the summer between sophomore and jr year in high school.
I ended the spring semester as my birth name and began the fall semester going by my name. It was incredibly awkward at first, especially the first class of the day and having to explain things to people. I didn't really have any friends, mostly just acquaintances, so no one knew what was going on except the teachers.
I talked with my school counselor about what was going on and how I would like to be referred to as such and as a male. An email was sent out to my teachers a couple weeks prior to the first day.
One of my teachers actually asked if I could come in to talk the week before, telling me that he understands what was going on and that he has my back and will be there if I needed anything. He is actually the reason why I pushed through and have the courage to even step foot inside the school. I have always been bullied all through grade school. There were some obvious comments made by many people throughout the year, none of the teachers would single them out mostly because they just did not know how to handle it. Then there was my algebra teacher who encouraged gay jokes in his class.
Long story short, I have heard from others and have noticed it myself that there is usually someone who will stand out and have your back and it may be someone who you would least expect, like my one teacher watching out for me and even a few months before graduation another teacher spoke up and offered her assistance when I was going through some mental turmoil.
I had the option to use the nurse's bathroom if needed, and when it came to gym I actually took an online course at an university on the other side of the country to fulfill the credit. I took a bowling class that just went over the basics of bowling and had to play a certain number of games and what not. I knew for sure that if I were to take gym I would be bullied not only physically but emotionally as well. In middle school I was harassed by everyone including the female gym instructor. Even she got on my case and even marked me down a letter grade because I refused to change in front of people. While using the stall to change there were girls who would try to kick it open, climb onto of the wall, and even peek through the gap between the door.
Schools have come a long way to support students by having various options available to meet the needs of each individual student.
If you do not feel safe taking gym, it is a subject to bring up with the administration being that the student's safety comes first, though every administration in different and depending on whether your counselor is willing to take the time to find another option.
High school is a very tough place to transition in, depending on the environment. It takes courage to transition regardless, but maybe more so when in high school since it can be a very unforgiving environment, not to mention an awkward time in one's life.
The best advice I can give you is to have open communications about how you feel and what would make you comfortable and especially to feel safe. If a teacher gives you trouble, or even your counselor, go to the person above them and so forth, especially when it comes to a situation involving discrimination or harassment of any kind. I was told by many of my teachers/ instructors that they keep teaching because of the feeling of making a difference in a students life and seeing a student succeeded fuels their motivation to keep on doing so. Don't be afraid to seek assistance or advice from a teacher you trust.