Completed the recommended course of Duovir. Also I am noticing two small hard balls below my jaws. Also recommend on what all STDs I have to get tested before my marriage on 12th June. I am curious about your doctor's decision to begin treating you with antiviral medication 8 days after exposure. It is quite possible that the symptoms you were experiencing were related to the medication.
Many people have severe enough side-effects to warrant discontinuation of treatment.
While there should be no negative long-term effects for you taking the medication, it was probably not necessary and may have caused you additional anxiety. The first doctor's response sounded quite accurate and reliable. Get tested at least three months following your exposure for an accurate result. Different sources will suggest waiting anywhere from 3-6 months to get tested. It sounds like you are quite anxious about this experience.