Follow-up questions should be part of the same thread, not new ones. Only a limited number of new questions can be accepted daily, so I deleted yours to make room for others.
You're asking questions that would take a 5-page essay to answer. Please read up on BV; I don't have time to write a mini-textbook. Information is available on many websites and in medical libraries. But in general you are overreacting. You are the guy. If your partner has BV, that is her problem and I would be happy to entertain her questions. There is no reason for you to suppose you are infected or have any problem related to her infection.
There is no such thing as BV in men, thus no diagnosis for it in men. In women, the diagnosis is based on a combination of clinical findings and microscopical tests; there is no single test for it.
I already told you above that doxycycline would have cleared up chlamydia (for sure) and gonorrhea (probably) if that were your partner's underlying problem.
I don't provide specific treatment advice on this forum; that's too close to practicing medicine from afar. But the usual medications used in women with BV are metronidazole (Flagyl and other brands) by mouth or clindamycin vaginal cream.
HHH, MD
I'll try to help, but I'm not sure it will have the benefit you hope for. Bacterial vaginosis (not 'vaginitis') indeed seems the best bet. I base that on your partner's symptoms, which were classical for BV: thin discharge with odor, with maximum symptoms (especially odor) after sex, is straight out of the textbooks. Trichomonas can cause similar symptoms, but the negative test for trich rules that out. Cleaning away secretions before testing (or not cleaning) makes no difference in any of this.
Most of the other information you provide is not helpful one way or the other. The microscopic results you describe, i.e. the various kinds of bacteria seen under the microscope, are typical for BV but also can be seen in perfectly normal vaginal secretions. There is no test for BV in men, and there is no clear male counterpart. I don't know what test was done on you, but the result is meaningless.
I hope your partner was tested for gonorrhea and chlamydia, because some cases of BV may be triggered by those STDs. But if not done yet, it's too late: the doxycycline would have cleared up those infections and testing now won't help.
The origins of BV are obscure. It tends to be associated with all the markers that suggest STD, such as being more frequent in women with multiple partners and after sex with a new partner. But despite extensive research, no male counterpart has been found; the male partners' examinations and all lab tests are entirely normal; and treating affected women's male partners makes no difference in whether the problem persists or recurs in women. At the same time, some couples report that if they avoid sex for a while, or use condoms consistently, the BV clears up--but usually even those things make no difference.
There are several treatments for BV, but doxycycline isn't one of them--I'm not surprised it made no difference. The greatest success tends to be with metronidazole (Flagyl), although vaginal clindamycin is often used. Your partner should follow up with her health care provider; or, if not certain of his or her expertise, seek referral to someone else, such as an ObG who specializes in infectious diseases. Such specialists generally are available in major medical centers and larger metropolitan areas.
Best wishes-- HHH, MD