Given your sexual history (and your partner's) and negative recent STD testing, you probably can pretty much disregard the possibility of an STD as the cause of your symptoms. HPV certainly wouldn't do this. If you told me the discomfort came for say 3-7 days, then cleared up entirely, then recurred say 1-3 months later (with the same pattern each time), then I would be concerned about herpes--but that seems unlikely.
Urine cloudiness isn't an STD symptom, and everybody's urine is cloudy from time to time. It depends on diet and fluid intake, and on urine pH (acid-base balance). The next time you notice cloudy urine, try adding a few drops of vinegar or lemon juice to a urine sample; it probably will turn crystal clear.
Bottom line: all I can suggest is that you see a health care provider if the discomfort persist, or of course if you develop other symptoms like overt sores, discharge, etc.
With regard to HPV, you can be 100% certain you are, or have been, infected with your partner's HPV strain. There is no way to know whether she had it first or you did, but that doesn't matter. There is no reason for the two of you to be using condoms for STD/HIV protection (but of course it's fine as contraception). But if you weren't infected and hoping to prevent HPV, this business about brief insertion then using a condom makes no sense at all.
Good luck-- HHH, MD
I think I misunderstood the condom business, i.e. the condom business was before her HPV infection, right? Sorry. Anyway, at this point using condoms won't make any difference in her HPV infection or yours.
HHH, MD