I went through this--in some ways, I am still going through it. I'm still here, and I'm not doing too badly. Okay, I didn't have a problem with acne, but I lost weight and still kept thinking I was too rounded and girly. My voice was a tenor, and I wanted a baritone. I thought, and still do think, that my face isn't male enough. My chest bothered me no end--I had been trying to ignore it for so many years that once I really came out and started T and was starting to "pass," I had to have top surgery immediately. I'm lucky I had the funds.
I was struggling to do well at my job, but everything took such an effort. I kept telling myself that someday I would turn that corner, stop obsessing 24/7 about trans stuff, and start having enough emotional energy to do well at work. I was right. I'm not there yet--I still obsess; sometimes grading papers is like pulling teeth; some days I get very little done--but I'm getting there. I learned to talk myself through stuff, confide in my therapist and leave messages on his machine to sort of bootstrap myself, and see supportive people as often as possible.
I don't know if you're in therapy, but I hope you have support groups or friends to see. It really can help to be around other folks who understand or at least try to understand. There are good times to be a hermit, but I don't think this is one of them. If people are reading you as male, then that's a reason to leave the house and rent a video (Netflix doesn't count) or go run an errand or meet a friend at the coffee shop.
Your skin will settle down eventually--have you seen a dermatologist for that? Just keep telling yourself that you're a teenage boy, and teenage boys get zits, and you won't be an adolescent forever. In truth, lots of people don't even notice or care about the acne. Especially people who already like you.
Oh, another technique I still use is to look back and see how far I've come. I came out. I got a therapist--no small feat for me--and went to support groups, which I was terrified to do. I even made a few new friends and stopped hiding in my house all the time. I started HRT, and I enjoyed the changes, especially my voice. I like to put on a CD and sing along to a favorite song; I sound SO much better now than I did before HRT, even though my voice is still settling down.
I don't know what to tell you about school. Can you withdraw and go back later? They might understand if you lay it all out for them.
Anyway, keep trying, see other people, and try to accentuate the positive whenever possible.
