Yes, looks like instead of copying the contents of the upload folder into the forum folder, the upload folder iself was copied. So all the files were in the upload folder on the server rather than the base folder for xenforo.
It's surprisingly easy to do that... makes me wonder how confusing...
I get:
Mysqli statement execute error : Table 'xf_cz_userchange_log' already exists
when I try to update. Tried to uninstall and then reinstall -- same problem.