Believe the tests. You are unlikely to have the diseases you were tested for, in part because your exposure was very low risk and in part because the tests are negative. Tests for syphilis, herpes, HIV and hepatitis (B&C) may take more than 10 days to be positive but your risk is so low that I am sure you do not have these diseases. Realizing that you will probably get tested anyway, when you have negative test results at 8 weeks you can be sure you do not.
Those little bumps have probably always been there and are called "pearly penile papules". All men have them although they vary in size from person to person. They are not herpes. EWH