You might want to get your prostate checked, if it is inflamed it will cause slight burning sensations when you urinate.
Just out of curiosity, what could "normal bacteria" be consist of? I understand that this is a non-STD bacteria, but how would one obtain a bacteria?
It sounds like you have a knowledgeable doctor; I suggest you just follow his advice and assessment. Your negative test results pretty much rule out any STD that would cause the symptom. If you want to be extra certain, the best approach is to suggest your partner get tested for common STDs and vaginal infections, rather than getting additional tests yourself. Of course if you develop other symptoms (discharge, sores, etc), or if your partner has any symptoms, return to your doctor. In the meantime, I see no reason you cannot resume or continue sex with your partner.
Nothing you say suggests a need to test for HIV any sooner than usual. Once a year probably is about the right frequency for HIV testing.
Good luck-- HHH, MD