I wanted to wait until marriage initially, but...

I am 16. My boyfriend and I wanted to wait until marriage initially, but of course in the moment these kind of things are easily forgotten. 4 days ago (Friday) we had sex for the first time. We didn't have protection at first and it just sort of happened but we stopped after not even a minute to be careful. Then we got condoms and had sex again, and Saturday again with protection. My period was due today but it didnt come. I had very bad cramps earlier that i ONLY get on the day of my period, as well as extreme fatigue. However im fairly certain my calendar is early because I was 3 days early last month. My period is rarely perfectly on time anyway, but this stress is eating me alive. I dont regret having sex or anything, my boyfriend has been my best friend for years and I'm certain we'll be together for a long time. And even if not I won't regret anything because it was still out of love. I'm just extremely worried about being pregnant even though we were very careful, I tend to be paranoid about several things. The only thing really worrying me is after he finished (inside the condom) he went back inside me, unprotected, a few minutes later, but just for a second because I got nervous. I have read that heavy stress can delay your period and I really feel like that is what's happening here. I can't stop worrying plus I have exams next week and I'm trying to pull my grades up so this is the worst possible timing. I don't want to talk to my parents about this, but I have been confiding in my best friend who is much more experienced than I am with sex. I really came here for some second opinions but mainly support to ease my mind a little so I can stop going crazy. Your responses are much appreciated!