I'm sorry to hear about all of your pain, especially since you are 16 and still a "minor " and under your parents care. ( or seems lack of Care to me )'
Your High School should have a School Nurse and a Counselor. Maybe you can go talk with one of them ? I'd try the Nurse first. I would sit down with him or her and explain what has been going on with your body. See if they can come up with a possible reason for all of your symptoms. They are Not Dr's but are well trained in Children and Young Adults Bodies..
Ask if they feel you should have a check up with your Family DR and if they say yes, ask them to put it in writing. This way should something serious arise, you have proof you asked for help.
If your parents still do not take you to the DR. Then they are Neglecting you.
Even though you are 16 and they know you are sexually active, Child Neglect is a Criminal offense and in the eyes of the Law, you are still a Child. It is your Parents responsibility to maintain your Health, ensure you are safe and protected ( medically as well as normal care ).
Are you using Sexual Protection ? If not ask your Parents to take you to the DR. For some form of Birth Control.. While there talk with the DR. about the other issues.
I am Abhorred at the fact that your parents do not feel that your pain and headaches and even your sexual activity is not a Life or Death Issue
It is possible you could have a tubal Pregnancy or a STD or other Infection.
Sit down calmly with your parents, write down the symptoms, how long it's been going on, how and where the pain is and simply ask them to take you to the DR.
If they say No, then when the pain gets bad, tell the Nurse at school they refused. She or He will be able to help you find some help with this issue.