My head was hurting before i got a flu shot was it safe to take 2 aleve (naproxen) for the pain? i think i slept wrong?

Yes it's OK: You are ok treating your headache. However, there have been some studies which indicated that use of anti-inflammatories, even tylenol (acetaminophen) within 24 hours of an immunization may decrease the effectiveness of the shot. You might consider using non-pharmacologic methods: massage, a heating pad or pack of ice (whichever temperature seems to work best for you.) or try taking a better nap today.