As Alias Lola responded (below) before I did, it is more likely that you acquired the infection in the several days before onset of symptoms, not several months ago; and therefore that your current partner is chronically infected and you got it from her. If a blood test has not yet been done, get it done immediately. If it is negative for HSV-2 (or only weakly positive) and becomes positive on repeat testing in a few weeks, it will prove recent acquisition. In the meantime, your partner also should be tested. My bet is that her result will be positive for HSV-2. (All of which makes her initial reaction ironic--but be sensitive about how you address it with her.)
By the way, I hope your doc did a herpes culture--but since you say nothing about it, perhaps he didn't. That was a mistake; it is very important that you know the virus type. The blood test will do that, but the culture would have nailed it down with certainty. Whether your herpes is due to HSV-1 or -2 has a huge impact on what to expect in terms of future recurrences, and the risk of transmission to (other) sex partners.
Your doctor was being overconservative about condoms; and doesn't know what he was talking about in relation to "immunity to Valtrex" (or didn't explain it to you clearly). But more important, there probably is no need to take steps to protect your current partner at all; as suggested above, she probably already is infected. In that case, she is immune to re-catching the same virus at any body site; there would be no restrictions whatsoever on what you do sexually. For aesthetic reasons, you likely will want to avoid sex if/when you have recurrent sores, but even that would pose no danger of transmisison.
Bottom line: follow through on my advice above about diagnostic testing for you and your partner. The results will be the primary guide to the necessity of prevention and which methods are most appropriate.
Good luck-- HHH, MD
Your symptoms seem more consistent with an initial herpes outbreak, as opposed to being in a carrier/latent state for several years. It's quite possible you were infected by your current girlfriend, if you're truly in a monogomous relationship. I don't think a recurrent outbreak would present itself with fever and swollen lymph nodes.
But I'm just Lola....
Dr. H is the expert.
Forgot to mention, that most people do not know they are infected. So, I wasn't insinuating your girlfriend could be infected and knows it.
Lola is right.
I meant to say outright that you might want to seek out a doctor who knows more about herpes; I sort of implied it by criticizing his apparent herpes knowledge. If you are in a major metropolitan area, you probably can find an infectious diseases specialist; or go to your local health department STD clinic--or call the clinic to ask which private providers in your area are best up to speed on STDs.
HHH, MD
A couple more thoughts in thinking about my replies: It is even more important than I said above that you get laboratory confirmation of the diagnosis. On reflection, the slightly atypical location of your herpes lesions (base of penis) combined with your doctor's seeming unfamiliarity with the disease makes me wonder whether the diagnosis is right. Getting swollen glands in the neck in association with genital herpes is rare, unless you also had oral lesions; the location of lesions in or near hairy areas might suggest things that can be confused with herpes, such as folliculitis; and the apparent response to Valtrex could be coincidental, since folliculitis will clear up quickly on its own and something else might have caused your fever and swollen glands in the neck.
All of which reinforces the importance that you have proper diagnostic testing ASAP.
Good luck-- HHH, MD
Thank you! I'm looking for an M.D. now.