Welcome to the STD forum. I'll try to help. The bottom line is that I doubt your symptoms are due to HPV or any other STD and I do not believe your girlfriend is at risk for anything you could transmit to her.
Genital-genital contact could theoretically transmit HPV, but usually does not, and your anal sex experience was condom-protected. Even if the condom failed, your risk there was for HPV of the anus and rectum, not the penis. Your PA did not think the penile bumps are warts, and you even acknowledge yourself they don't look like typical warts; combining that information with low risk of exposure, plus your belief the lesions look like sebaceous glands, I guess I don't understand why HPV and warts are even on your mind. As time passes, minor variations in penile skin are normal and sebaceous glands might well appear more prominent. It doesn't mean anything. Of course, I cannot say you don't have HPV, since all sexually active people acquire one or more genital HPV infections; having genital HPV is a normal and expected consequence of human sexuality. But most infections are asymptomatic and cause no harm, and if you have it, there is no relationship to the symptoms you describe.
As for your other symptoms, they really don't hint at any STD, and your multiple medical evaluations and negative tests assure you don't have anything. If the symptoms continue and you remain concerned, see a health care provider about them. But you can put STDs aside.
To the specific question:
1) I'm not convinced there is anything abnormal going on, or that you have any condition for your immune system to get control of. Certainly not HPV or any other STD.
2) Either wait it out or see a provider, as I suggested above. Your choice. There certainly is no danger in waiting, except perhaps for the anxiety factor.
3) In general, the high-risk HPV types -- the strains associated with cervical cancer -- tend to persist longer than the types that cause warts. But this issue is irrelevant to your situation, for the reasons discussed above.
4) Your resistance notwithstanding, I am convinced of my judgment.
5) Stop examining yourself so closely. A "new bump" could be another sebaceous gland or other minor variation in your skin.
I have to wonder whether the main problem here is emotional. Maybe anxiety or guilt about your sexual choices? Ambivalence about tendencies toward sex with other men? Please think about it and consider discussing it with your primary care provider.
Best wishes-- HHH, MD