I may finally be tying it all together.
What all of this says is that Acyclovir uses phosphates to inhibit viral replication.
Image of Acyclovir inhibiting viral replication: http://escholarship.org/uc/item/2vz9c4hz/vistmech.jpeg
As noted much earlier a Calcium pump is used for Herpes to enter/exit a cell so more calcium ions eject herpes and fewer calcium allow herpes to enter. However, Calcium and Acid (H+) suck up available phosphates (Calcium Phosphate). In essence, Herpes has hacked its way around nature so that it can enter cells and not be stopped.
I have been using Calcium to throttle and stop Herpes outbreaks, but I have not been adding neutralized phosphates. I have begun adding Phosphoric Acid (20 drops) and baking soda (1/8 tsp.) into the mix and alternating in Calcium weekly by stopping phosphates for a day, then taking calcium for a day, waiting a day, then starting phosphates. I have just begun (12/7/13) and will post findings, but so far so good.
WARNING: Kidney stones are often Calcium Phosphate so I am drinking plenty of water while attempting this and attempting to avoid overlapping Calcium and Phosphates treatments.