I’ve seen that sort of behavior when script-kiddies run something they found on a haxx0r site. Some times it results in an “index.html” file being uploaded to your directory. Since there is an order of precedence for what files Apache loads as default, this page will override your index.php page.
If that’s what happened you may not have actually lost the files you started with. While your method is sound in terms of making sure all the sketchy files are gone, a fresh install of the CMS will not have any 3rd party add-ons or modules that you installed.
This isn’t a problem if you didn’t install any, but the site won’t run off a restored database if you did have extensions. This can be somewhat of a foo unless you reinstall every extension before restoring your database backup. With most CMS exploits I’ve encountered it’s typically 3rd-party extensions that are compromised rather than the core CMS code. That’s why I suspect there may be extensions for your site.
I’d grab some copies of the various automatic backups of your website soon. You might be able to get a copy prior to the exploitation, but it’ll be overwritten soon if you grab nothing. You might not need those backups, but better safe than sorry.