I have had this clicking noise in my head for years! I am 19 now, and I remember telling my dad many times after coming down the stairs from my room and jumping in place that the top of my head was clicking. It does sound like clicking two fingernails past each other, almost like a suction, like if you touch the tip of your tongue to the roof of your mouth repeatedly?
My dad told me when I was younger that the amount of fluid in my cranium changes very slightly, depending on hydration, etc. I imagine my brain being just a little too small for the area in my skull and that is the sound of my brain hitting the top of my head when I walk down the stairs. My brother was born missing a portion of his brain and didn't find out until he was over 20. I worry that I have the same problem! The explanation of the small flap where your skull formed as an infant seems likely to me. I do not hear the clicking in my neck or side of my head/ears. It seems to be coming from the tippity top of my head!