Unless you changed something, the default location of your files would be /home/Your_user_name/www.your-domain.com
If you're seeing the directory listing & know files, that means they were uploaded somewhere else, as seen with the 404 error you get when you try to go to a specific file.
When you connect with an FTP client, you should see a domain.com directory for your domain. If not, be sure you're logged in as the user the domain runs under.
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