The small bump at the base of your shaft sounds like an ingrown hair because herpes doesn't have hair in the blister/bump. But then the second one sounds strange. If there is a dark center that doesn't sound characteristic of herpes and the pain is a symptom of herpes but it could also be another ingrown hair. It's best to go get a pcr test and an antibody igg blood test if it's been 3 mos. post possible infection. Don't feel too bad condoms don't really protect against herpes anyway. Herpes is a skin virus, it's not in the blood or semen. It is transmitted from skin to skin, and the person doesn't even have to have an active lesion to pass the virus. And if you do come positive it might make you feel a little better to know that 50% of generation y will have genital herpes by age 50 anyway, because of how tricky it is to diagnose. 90% of people don't know they have it, so just let the girl know who you had unprotected sex with. She may not know she has it. Just call her from a private number and let her know annonymously, but only after you get a positive answer.  Good luck.