Aperture never ceases to amaze me - not that I don't still love it. After once again backing up my main library, I tried rebuilding again. This time the rebuild "completed", but let the library in a weird state. It would not display any photos in any view. The number of files shown to the right of Recent > Rejected in the Library Inspector was around 1/4 million - approximately the number of photos in the library. Having go that far, I decided to see if I could get anywhere by pushing further, so I restarted Aperture and asked it to Repair (not Rebuild). The repair didn't take long, and resulted in my library being in pretty good shape. I still needed to reconnect a bunch of originals, but this helped a lot. There are still some bad links between Versions and Files - redoing the thumbnails did not fix them. For those, I need to reimport, and then Lift and Stamp onto the reimported ones.
Even crazier: the project I had deleted and was attempting to import showed up in my library!
I think we need to maintain a detailed list of features required in Photos to make it a passable substitute for Aperture, and keep bombarding apple.com/feedback with it.