I think I qualify as knowledgeable on the subject. I've had the tick twice now on my '03, but the explanation listed above in the 03/04 Cobra FAQ is spot on.
The theory on the tick is that it's caused by a poorly designed coolant passage on the rear of the head. This coupled with a equally bad design for coolant routing out of the drivers side head allows the valve seals on the number 7 & 8 cylinders to wear enough to let them cant just enough in the guide to cause the ticking. So far no one has reported any long term effects from this problem, besides the annoying sound it makes. The ONLY fix is to replace the head with the latest casting from Ford.
U.M.