I do have a backup of the original log files from the original server.
When the InnoDB tables weren't working, I took the old ibdata1 file
and uploaded it to the new server. That fixed a portion of the
problem, but not everything.

Things are being done too inconsistently. If you want to download the files via sftp, login to mysql first and lock all tables as mentioned in the previous email. You'll want to download everything, including the innodb transaction logs, innodb data files (ibdata* if using default naming), and the actual database directories.

The ideal solution would be to take a mysqldump. You can actually do that through phpmyadmin.

If binary logging is enabled, you don't need to download those.

-Matt
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