If this were happening to me I would do a little experiment and have my wife take a load to the throat. If it burns the Vagina it should burn the throat/mouth/stomach, right? Then I would know for sure if its me or if its her PH levels or something(anything) that is wrong with her Vagina.
Seems to me like y'all could get some more reliable answers if you swallowed your own load. You don't even need gymnastics, just do your deed and slurp it down, smear some on your face. Make sure you don't wash yourself first, gotta get some taint funk in there.
Anyway, it looks like phenibut is excreted unmetabolized, and as an amino acid, it would buffer pH around neutral. But a pH difference would be pretty extreme to wind up burning, and wouldn't last for days.
I can't imagine phenibut itself causing burning, even if you dumped a full dose, but then it wouldn't last that long either.
Have you considered that maybe after going through a course of strong antibiotics and a yeast infection, your girl might WANT you to wear a condom, at least for a while?
Alternatively, quit the phenibut and see.