Remove past versions from Spotlight searches?
I ended up copying all of my documents (I didn't really have that many) out of iCloud to the local disk, and then deleting them from iCloud. The old versions were still showing up in Spotlight, so I added the entire drive to Spotlight's Privacy list to delete the index. Then I put the documents back into iCloud, removed the drive from the Privacy list, and let it sit for a few hours while it reindexed everything. After two days of usage everything seems to be working normally once again. Thanks to @bmike for the ideas.