'Access Denied.'

Have you reviewed all of these resources?
https://codex.www.ads-software.com/FAQ_My_site_was_hacked
https://www.ads-software.com/support/topic/268083#post-1065779
https://smackdown.blogsblogsblogs.com/2008/06/24/how-to-completely-clean-your-hacked-wordpress-installation/
https://ottopress.com/2009/hacked-wordpress-backdoors/

Yeah I fixed everything, code wise. And just sent it back to Google Webmaster to get cleared. Once I tried going to it, the ‘Access Denied’ came up but I have yet to find anything wrong.

Have you asked your hosts about it?

I was told to contact the Security team tomorrow. I tried to troubleshoot again by myself and somehow the index.php file permissions was 200, so I changed it to 644. But then I attempted to open the blog up and this text appeared.

“Warning: include(/homepages/35/d309942428/htdocs/blog/wordpress/wp-content/themes/WP-Photoria/index.php) [function.include]: failed to open stream: Permission denied in /homepages/35/d309942428/htdocs/blog/wordpress/wp-includes/template-loader.php on line 43

Warning: include() [function.include]: Failed opening ‘/homepages/35/d309942428/htdocs/blog/wordpress/wp-content/themes/WP-Photoria/index.php’ for inclusion (include_path=’.:/usr/lib/php5′) in /homepages/35/d309942428/htdocs/blog/wordpress/wp-includes/template-loader.php on line 43″

Not great with code, so I am quite sure what I am looking for.

Sounds like you have a whole stack of permissions issues here. Best leave to your hosts to try and sort out what happened.