Releasing the sludge/stones, but not having done the coloncis or at least a colema (inexpensive on ebay) afterwards is certainly a great risk for developing the symptoms described. I have seen the same or similar in hundreds of people. Also the kidneys and lymphatic system get affected by all that (I have described the conneciton liver - digestion - lymphatic system in detail in The Amazing Liver Cleanse. Make sure to do the kidney cleanse (see same book ) every 3-4 liver cleanses.
The Herpes virus is harmless unless the immune system is weak. Viruses don't attack cells unless they are already undernourished, weak or damaged. They help prevent many cancers. Viral disease is not what it is made out to be. Diet and lifestyle according to body type (see The Key to Health and Rejuvenation) plays an important role in keeping the immune system strong. Foods that are inapproapriate for one's body type keep engaging the immune system, and thus weaken it. Since over 60% of the immune system is located in the GI tract, not digesting foods well can affect over all disease resistance. Anxiety, fear and tension can do the same.
Pau 'd Arco and Astragalus are excellent immune boosters.