To be honest, I don't know why you are so concerned. Your ObG is exactly right. What if he had a wart? If you haven't developed visible warts by now from that exposure, you aren't going to; and even if you had an asymptomatic wart virus infection, it would have cleared up by now. Either way, at this point clearly you are home free.
As to your new bump, it sounds like a skin tag. But I can't tell for sure; see your ObG again if you remain concerned about it.
Looking at the title you chose for this question, indeed you are way 'over thinking it'. You need to read up about HPV and how much of a non-problem it is. Everybody gets genital HPV; it is inevitable and unavoidable, a normal part of being a sexually active human being. Most infections are asymptomatic, never causing either warts or an abnormal pap smear. It's just like having staph or strep bacteria on your skin and E. coli in your intestine: sometime those normal bacteria can cause serious infections, but mostly they just sit there.
Sexually active women should have the HPV vaccine, to reduce infection with the most common wart-causing and cancer-causing HPV types. And follow standard recommendations about pap smears. Otherwise, just forget HPV as a health issue in your life.
Good luck-- HHH, MD