You describe a highly atypical case, if indeed you have genital herpes. But I tend to believe you do not. More important, you have seen several providers, including all the appropriate specialists, including a dermatologist and an infectious disease specialist. In that context, it is unlikely that any distant online resource, including this one, can add very much. But my overall perspectives follow.
Most of your symptom simply are not compatible with HSV-2 infection. Genital herpes does not cause widely spaced lesions (most outbreaks occur in distinct, localized clusters, each outbreak within an inch of all the others); doesn't cause sores in the mouth; and can't be the cause of lesions that do not respond to antiherpetic drugs like Valtrex. If you have HSV-2, you also have something else (or more than one other thing); herpes simply cannot explain most of what you describe.
The positive culture (or similar test) for HSV-2 plus the eventual development of a positive blood test of course suggest you might be infected. However, it is equally likely that the culture test was false, as the ID doctor concluded. As for the positive blood test, if you will review many comments about HSV blood tests on this forum, you will learn that many weakly positive blood tests are false. (For example, see
http://www.medhelp.org/posts/show/593272.) Most people with inconsistent HSV-2 blood test results -- i.e., negative sometimes and positive others -- are not infected. Most likely the negatives are the accurate ones. But if your doctor wants to pursue this further, you could have an HSV Western blot test to learn once and for all whether you have it. WB is discussed in the same thread.
For these reasons, I tend to agree with the ID specialist that do not have HSV-2. If you do, it still does not explain most of the "outbreaks" or any of your other symptoms. Something else obviously is going on either instead of, or in addition to, herpes. I don't know where you heard of a relationship between STDs and autoimmune diseases; there is none.
What to do now? Most important is that you pick a single primary care provider who you trust and who understands your symptoms, even if s/he isn't necessarily a specialist in a particular area. Then trust that person to evaluate things further as needed, including referral to appropriate specialists. You might first discuss getting the opinion of a clinical immunologist. (That usually means a rheumatologist, i.e. arthritis specialist; they are the ones who deal with autoimmune conditions.)
I hope this helps. Best wishes-- HHH, MD