HPV 31 is not contained in the HPV vaccine but the vaccine should help to protect you from infection with the types of HPV contained in the vaccine (the MERCK vaccine contains HPV types 6,
and 11 which cause most visible genital warts
and HPV 16
and 18 which cause about 2/3 of cervical cancer in women)..
Regarding your HSV-2. Your blood tests are both positive and, presuming you were tested with a type specific test, I suspect that this is indicative that you have HSV-2.