The morning after pill has a large dose of hormones in it, so it will come with side effects. It is not fool proof. With the pill, you are expected to follow-up with your doctor within 3 weeks to verify the presence of pregnancy or not. You should call your doctor and schedule that appointment to be seen. They can perform a blood test to check for pregnancy.
Okay, having sex leaves you with a chance of pregnancy, from what you have told me I can't give you my opinion on how likely it is, but it sounds alot like you are having the side effects of the emergency pill... So wait it out and maybe take a test to help ease your mind. But as I said, that pill has some nasty-pregnancy sort of side effects, just use a condom next time and save all this hassle(harder done than said I know) but it will be better for your stress levels which can also cause physical symptoms.