Having both recurrent yeast and BV is unusual, so one of my first thoughts is to wonder whether you really have both. You might discuss it with your provider, unless you're already quite certain. For the moment, though, I will assume you have both recurrent yeast infections and recurrent BV. Both infections can be related in part to depletion of normal protective bacteria from the vagina (primarily certain strains of lactobacillus). Whether the amoxicillin really was the initial problem is hard to say, but that antbiotic has the capability of destroying vaginal lactobacillus, so it is a possibility. Your vaginal pH indeed probably is "off" some of the time, but that is circular reasoning: it is lactobacillus that maintains normal acidity. (That is, reduced acidity may be a manifestation of the underlying problem, not a contributing cause. But there is a lot of scientific uncertainty here.
You are absolutely right that neither hygiene nor diet is the problem. Such issues as tight clothing (jeans in summertime) and diet influencing vaginal infections are urban legends. Ditto for re-using towels, direction of wiping after urination or defecation, etc. Given what I said above, it is simple common sense that putting lactobacillus into the vagina should help, right? Problem is, no commercial lactobacillus preparations contain the right kinds of lactobacilli. The strains common in dairy products (L. casei, L. acidophilus) do not survive in the vagina and have no preventive or curative effect; eating yogurt (or douching with it) is useless, as are lactobacillus products you can purchase in health food stores. Intensive research has been going on for a decade to convert the protective kinds of lactobacilli into products that will successfully colonize the vagina, but to date success has been spotty at best. So maybe someday, but not yet.
So what do you do? The yeast part is easiest: most women with recurrent yeast can take fluconazole (Diflucan) once a week and completely prevent symptomatic infections. If this hasn't been tried, you should discuss it with your ObG provider. Such preventive treatment appears to be safe and usually remains effective months or even years on end.
Unfortunately, I can't be so optimistic about recurrent BV. The syndrome is not an STD, but is associated with sexual activity, and some women say they stop having problems if they and their partners consistently use condoms. Another issue, which may or may not apply to you: you don't say the sex of your partner, but among lesbian women, BV clearly is sexually transmitted. That is, when women share their vaginal secretions through hands or sex toys, if one has BV, the other always has BV. But one of those partners might have a mild case and be asymptomatic, so it isn't obvious. In such circumstances, treating both partners simultaneously might help, perhaps coupled with abstinence for a few weeks, or limiting practices (barriers etc) to avoid vaginal secretion exchange.
From a clinical perspective, I cannot link your vaginal infections with reduced sex drive--except for the possibility of stress or anxiety as a contributor. But sexual functioning per se is outside my expertise. Sorry.
This is a scientifically complex area, frustrating for patients and providers alike. I hope this information helps.
Best wishes-- HHH, MD
The general sense that vaginal inflammation or infection might increase the risk of cancer or other reproductive health threats is outmoded by a couple of decades. It may be true, but the emphasis in recent research focuses on specific infections, not the general case you suggest. To my knowledge no data have linked recurrent yeast to such outcomes; and BV actually does not cause inflammation. To the extent there is risk, it is small; there is nothing in your story that makes me concerned about your future fertility.
Congratulations for keeping a very level head about all this, regardless of the frustrations--i.e., maintaining skepticism about all the old wives tales!
As far as specific suggestions, I already suggested you discuss weekly fluconazole with your provider. If you are using any vaginal products of any kind (douches, deodorants, etc) totally stop any such stuff. (Douching in particular is a common cause of BV--and women can get into a vicious cycle, believing that douching will control symptoms like odor and discharge, but it just perpetuates the problem.) Finally, you can ask your ObG to refer you to an ObG colleague with particular expertise in infectious diseases; such specialists are available at most large medical centers, especially if affiliated with a medical school.
HHH, MD