13wks pregnant. ive had an uri and a sinus/ear infection for the past two weeks. im on amoxicillin and my ear is getting much better but ive had a headache all day for days. by my ear/sinuses and the back of my head. all over. normal?

It sounds like the normal progression of the disease which was probably a middle ear infection. Amoxicillin will indeed help sterilize the infection from the middle ear but it is not unusual for you to have those symptoms as the fluid from your middle ear begins to clear. This can sometimes take up to 4 weeks for the fluid to completely clear. If your symptoms worsen see your doctor.