You will think I am crazy... but,
When she indicates "her vagina is hurting"... how does she do this? Does she point down there and say it hurts; or does she cry in agony and yell/whine it hurts? My daughter used to wake up an hour after she fell asleep (very sporadically, just as you describe) literally writhing in pain. It was spasmodic pain.. not constant. I tried baths, too, and sometimes they seemed to help, sometimes not. We went to the doctor I don't know how many times... swabbing for or trying to get a clean catch to check for UTIs. Were prescribed medication for yeast infections. Etc....
I finally had had enough of watching her suffer, and just knew in my gut that the doctors had it all wrong about UTIs and yeast infections, etc... So I contacted MY gyno's office. Spoke to the nurse/midwife practitioner there, and she suggested I take my daughter down to the children's hospital an hour away, to look at some other possibilities (she was thinking improperly formed internal parts--like a shortened something or other-- might be causing the problem). We went.
My child, who had been potty trained since her 2nd birthday, and NEVER had accidents, even over night, and never had ANY potty issues, and was still using the potty every day---- was constipated.
Yep. Constipated. Quite heavily impacted, actually. She still pooped every day, but the doctor said that perhaps she hurried and rushed things a bit too much, and only went enough to stop the urge and not to fully eliminate everything that needed to be eliminated each time. So over time, she was getting impacted.
Her sporadic pains were being caused by the impacted poop pressing against her bladder, causing it to spasm. Now THAT is painful! The regular docs missed it, because they simply asked me if she pooped regularly. Which she did, and I said as much. Well...... the xrays proved that she wasn't getting the job done.
If this sounds like it might be the case with your daughter, I'd be happy to share what the doctor told us to do to remedy the situation. Just PM me.