I don't know what is going on with my body

Hi so I am 18 and a freshman in college and I am seriously so scared because I don't know what is going on with my body. Okay so my last period was on 9/23/13 and finished on 9/27/13. Then on 10/9/13 I got the nexplanon implanted in my arm, and my DR. Told me to use condoms for a week just in case. On 10/11/13 I had sex with my boyfriend but we didn't use a condom (shame on us) and on top of that he finished in me. Since we thought the damage was already done (Silly us) we continued to have sex multiple times a day, for the next four days, and always finished in me. (Constant sex because we haven't seen each other over 5 months) So on 10/18/13 I took a HPT which was negative. And after that week I've been so tired, extremely moody, slightly queasy on some days, and I had back pain. My period was due on 10/21/13. I have a roughly 28-29 day cycle and always on time. Never skipped a period before even when I was on the pill. About 3 days before my period was due, my breasts were sore which they always get like that before my period but then after the 21st, they stopped hurting. I got serious back pain that then turned to chronic body pains on the 24th, and woke up with a sore throat. But on the 25th they stopped and my sore throat went away on the 26th. I am constantly hungry now and I just almost cry at anything now. On the 25th I noticed brown spotting everytime I wiped, and then it was gone until evening of the 26th, and it came back a little more than the first time so I had put on a tampon but when I took it out there was just a little bit of brown discharge. No actual blood. I took a second HPT on the 24th and it came back negative. I am just freaking out. My period is 6 days late and I really don't know what to do. I can't really go to a clinic because I'm away at school and don't really have a way of getting to one. The tests that I took were clear blue but I just got a third test that is the rite-aid brand. When should I take the test? Have any of you went through what I'm experiencing? What were your results? Maybe I am pregnant and my hCG is just too low? Also, I know I will be criticised about my poor sex decisions and yes I am aware of what I did. By the time I had sex it was 2 days past of my fertile days or whatever. That is what an ovulation calendar said to me. Anyways I am not sure, and please just give me advice as woman to woman. Thank you