Hi M23,
I just picked up this thread. Did the Children's doctors talk to you about doing additional testing for primary immune deficiencies or autoimmune disorders on your little guy? Don't mean to scare you, but oral herpes to the extent your son had them (from the sounds of your posts) is kind of uncommon in children, depending on the type of Herpes virus he was infected with (there are several kinds).
Any idea how or where he contracted the virus? Did your son ever have Chicken Pox (Varicella zoster, which is human herpesvirus 3)? If so, reactivation is what causes of shingles (same virus), but it's REALLY rare in kids (usually occurs in adults over 65), and usually appears along a single dermatome (nerve branch) on the trunk (not that it can't appear in the mouth, it's just a lot less common). Reactivation can be caused by severe stress or immunity issues.
Could your son have been infected with Epstein-Barr virus (human herpesvirus 6)? Most of the population is infected with EBV as young children, so there's a decent probability of this, but I would think he'd have had other symptoms, too, and the docs would have tested for EBV and also CMV (yet another herpesvirus) specifically. EBV could cause severe mouth sores and pain, but again it's pretty rare for young symptoms to have overt symptoms to EBV without some other underlying other pathology. Most children have no or very mild cold-like symptoms with EBV infection. Nastier symptoms are usually seen in teens and adults (infectious mononucleosis).
Herpes simplex I (HSV-1) is a very common virus in the population, usually occurs in the mouth and on the face, but is usually mild. Again, severe cases usually occur in people who have autoimmune diseases or immune deficiencies. HSV-2 is also common, but is usually associated with sexual activity, although if you're infected, it could have been transmitted to your son during birth if the infection was active. You could be infected and never know it, and could have been having an active flare during birth and not known it either, so don't feel guilty over this one (or any of the others, for that matter).
If your kiddo is normally very healthy, then this could have been just been some really weird fluke of a response to whatever other virus was causing the nausea and vomiting symptoms, or he had a coinfection with another virus and one of the herpes viruses, which was just too overwhelming for his immune system to handle this one time. If his health history shows a propensity for viral or bacterial infections, however, you might want to talk about this with his pediatrician.
I'm glad to hear your little guy is doing much better now, and that you're all coming out of the other end of what sounds like a really horrible experience. Good for you mom, for holding it all together!