Solved! But it wasn't pretty. In case it's helpful to others, here's how I solved it:
I finally got desperate and in the preferences, disabled iCloud Photo Library, then after a few minutes, re-enabled it. When I re-enabled it, it said I had 86 "referenced files" that it needed permission to access. After some Googling, I realized that referenced files are files that don't live within the Photos library folder, but that are linked to. It then told me to find these referenced files and pull down File | Consolidate to bring them into the Photos library. It did not tell me *how* to find them, but I got creative and made a Smart Album of all images with type "referenced."
The smart album revealed the problem images, but when I selected some and pulled down File | Consolidate, Photos said it needed permission and told me to navigate to ~/Pictures/iPhoto Library/Masters/2012 and put up a file navigation dialog. So the "referenced" files were still in iPhoto! Huh? My other 20,000 images had migrated over just fine. No idea why this was. But here's where the 2nd problem began. I *could not* navigate to that folder, since "iPhoto Library" does not appear in the Finder as a folder. So the dialog was telling me to do something impossible.
After puzzling on this for a while, I realized that the problem could be solved by deleting the references to external files from Photos and re-importing them manually. I launched iPhoto and manually found all 86 images (they were from three albums and fortunately I'm good about titling and labeling, so was able to find them easily. I then exported them from iPhoto as full res originals, deleted the references in Photos, and imported the old problem images as if they were new.
Photos then churned against iCloud overnight. By morning, it had become unstuck, and the photos I've shot over the past week are now present.
So the problem was not the new photos, but some old photos that for some reason had not migrated over from iPhoto properly. And Photos was recommending a fix that was impossible to achieve the way it was instructing me to. What a mess.
