I'll try to help, but it cannot be very much. You have been examined and tested for common STDs--that is all I would have recommended, and an online advisor rare can tell what's going on if direct examination doesn't come up with an answer. Your symptoms really don't sound much like herpes. I suppose it is possible, but I expect your HSV test in a few weeks to be negative; or if positive, I would tend to believe you had it all along didn't acquire it during your exposure at the end of March.
That said, all in all this sounds more like yeast than anything else, perhaps a yeast strain resistant to the usual drugs. Amoxicillin and clindamycin might have contributed to increased risk of yeast infection. The flaky, peeling skin doesn't sound like herpes--but you should rely on your own provider's judgment about that, not the opinion of someone who cannot examine you.
Sorry I can't be more helpful. Best wishes-- HHH, MD
Thanks for your help doc!