I got the email for the DS-260 on 11/22, one day after the last update. Immediately filled it out and called the designated hospital to make an appointment. Turns out it takes a few days to register the DS-260 in the system, so I called back on 11/25 and managed to get an appointment for her medical exam on 11/30. The results take about a week to be processed and they go directly to the embassy so no worries about them getting lost in transit.
 
	 
 
	In the meantime we headed to the prefectural police station and requested the police certificate. We go back on 12/5 to collect this.
 
	 
 
	Also got extremely lucky and snagged an interview time for her at the embassy on 12/11. Somehow some way, it looks like everything will come together within a few days of each other.
 
	 
 
	Assuming everything goes well with her interview, we should have her visa ready to go just before our flight out of here on 12/20. Crazy that about a month ago I was panicking about all of this, and it all just worked out. Particularly in thanks to @Crazy Cat, who told me about direct filing literally moments before I submitted online. Feels like we pulled off the heist of the century or something.
 
	 
 
	Will post a final update once everything goes through and we are (ideally) at home in America.