Looks good.
Wow, my U9 is cold, never seen it even get warm. I am guessing its shorted inside or Gen Output is shorted. The fact that you can’t see any signal on Pin 9 (Fout*) of U9 is not good. Either U9 pulling/shorting it ground or STM32 is shot.
alys: thank you.
gtr: As alys said. Hook up some working battery (AAA, AA, 9v, CR2032…) to Nano Input and adjust VD to see a straight line and proper reading. This will verify if Input is working or not.
I think you somehow need to disconnect U9. Perhaps lift pin 14 VCC. I don’t like that is hot.
FYI: I know V2 battery soldered directly 
So its best to splice in some connector before you do resistance checks or soldering to avoid shorts.