Welcome to the forum. Thanks for your question.
Your story contains both support for the possibility of genital herpes (likely due to HSV-1) and against it. On balance, I am inclined to believe you don't have it. If you do, it is not the likely cause of your ongoing symptoms.
The majority new HSV infections cause symptoms within a week, usually 3-5 days, after exposure. The two week delay thus is atypical. Second, herpes doesn't cause the more or less continuing or very frequent symptoms you seem to have. Herpes outbreaks never occur more often than every several weeks, and are much rarer than that for most people with HSV-1; each outbreak lasts no more than 1-2 weeks; and between outbreaks there are no symptoms at all. And at present, it would appear your genital examination is normal. (I trust your doctor's judgment that your urethra looks normal more than your belief it appears more red than normal.) Further, it is not plausible that herpes symptoms would continue despite a month of taking valacyclovir (Valtrex). Finally, most people with postive HSV-1 blood tests have been infected for many years; most infections are oral, acquired in childhood, often without symptoms of recurrent oral herpes.
Those issues generally argue against genital herpes. That said, a physician's diagnosis -- and belief you had a lesion consistent with herpes. But really, that's the only part of your story that's really consistent with genital herpes, which is why I believe you don't have it -- and if you do, that it isn't the cause of your ongoing symptoms.
The thread below provides more detailed information about genital herpes due to HSV-1. Please read it; the information should be reassuring.
http://www.medhelp.org/posts/STDs/Recently-diagnosed-with-Genital-Herpes-HSV1/show/969931
At this point, my advice is to stop anti-HSV treatment entirely and stay off it for at least a few months. During that time, keep your eyes open for a more typical herpes outbreak, i.e. overt (easily visible) blisters/sores of the penis. If such lesions appear, get examined promptly in order to have a viral test (culture or PCR) from the lesions. In the meantime, I think you need to work with your doctor about other postential causes of your symptoms.
I hope this helps a bit. Best wishes-- HHH, MD