It sounds like you acquired nongonococcal urethritis (NGU) from your partner. Since you do not say she was treated, I assume she was not given antibiotics. Even if her standard STD tests were negative, she should have been treated; there are several causes of NGU that do not show up on "standard" STD tests. You don't say exactly what symptoms of urethritis you are having (most likely discharge, perhaps with some discomfort on urinating?)--but more likely than not, you simply caught the infection from her again because she was not treated. If you are confident she hasn't had other partners, and you haven't either, this is by far the most likely explanation.
It also sounds like you have balanitis (infection of the head of the penis), perhaps due to a yeast infection that could have been triggered by your antibiotic treatment. However, you partner's HPV infection has nothing to do with your symptoms. And all your other symptoms are irrelevant (back pain, blurred vision, fatigue, dark circles, "shooting pains", etc). They might be related to anxiety over all of this, but they are not caused by your recurrent NGU or any other STD.
Bottom line: Both you and your partner need treatment with antibiotics active against NGU, such as azithromycin or doxycycline. And to be really safe, you both should be retested for common STDs (chlamydia, gonorrhea); and a health care provider should examine your penis for possible balanitis.
Good luck-- HHH, MD
PS: A slim possibilty is Reiter's syndrome, a kind of arthritis that sometimes follows NGU and certain other infections. Reiter's syndrome can cause back pain due to spinal arthritis, recurrent NGU, and perhaps rib soreness. Reiter's isn't terribly common, so it's less likely than simple reinfection from your partner. But if the back pain is severe or persists, you might ask your doctor about it.
And I forgot to add that Reiter's syndrome sometimes includes balanitis and other kinds of skin rash. If your own doctor doesn't know much about it, or if s/he thinks it is a possibility, you might ask about referral to an arthritis or infectious diseases specialist. But don't jump to this conclusion too fast; if you indeed have recurrent NGU, you still need re-evaluation for common STDs and both you and your partner need antibiotic treatment.
HHH, MD