Another comment, not directly pertinent to your questions: I am a bit perplexed by your partner having protected vaginal but unprotected anal sex. STD risks are just as high, generally even higher, with anal than vaginal intercourse. It doesn't matter a whole lot for oral sex, although even there it would provide an increased measure of protection, given your conscious choice of a sexual lifestyle that is high risk from an STD standpoint.
It's hard to second guess a third party's test result--it would be difficult enough to do that even if you had more direct information. Some older chlamydia tests (less used than in the past but still used by some labs, lower cost) are prone to false positive results. And it would be a slightly surprising event to have 2 separate infections simultaneously, presumably both chlamydia and a bacterial UTI. The other factor is the reliability that she was a virgin before all this, because catching chlamydia from your partner, if indeed he used a condom for vaginal sex, is highly improbable. So if she has it, I would assume that in fact she has had other partners.
There is no way I can sort all this out. Most likely you and your partner both can rely on your negative chlamydia tests, especially if ae newer (DNA amplification) test was used; those tests are highly sensitive and don't miss many infections. Of course, you or your partner could have been infected and had spontaneous clearing. So my main bottom line is "Who knows?"
As to your specific questions: 1 and 2, see above.
3) The type of streptococcus that causes strep throat (typically group A strep) is an entirely different organism from the one that sometimes causes vaginal infection (usually group B). Even if one of you had an atypical strep, that scenario is a distant stretch. I would disregard it.
4) From the strict perspective of medical and transmission risks, I see no reason to inform your other partners. But take into consideration the social context: if they learn about these events they might believe that out of special caution and courtesy, they should have been told. So it's up to you.
Bottom line: The most likely scenarios seem to be either that her chlamydia test was false positive, or that she was not truthful about other partners--i.e., that her infection isn't related to sex with your partner. (With one caveat: As you likely know, UTI can be triggered by sex--not an STD, but the result of "massaging" bacteria into the urethra. That's what "honeymoon cystitis" is all about. But your partner has no biologic or ethical responsibility for that.)
I hope this helps. Best wishes-- HHH, MD