diff -u -r ~/ojs-2.4.4 /var/www/html/ojs > mods.diff
I have changed all the folders to 755 and files to 644 which is what php requires for functioning properly. Persmissions and ownership should not be a problem now.
The issue may be that their site is not compatible with the newer php. You are running php 5.3.28 and it is configured to run as suphp. When running like this, php runs as the user so since the files are owned by the same user, they have full write access to all folders and files.
This would mean that there needs to be a folder in their public_html called index.php because the url contains /index.php/. Now, in some cases, this could be functional via some kind of rewrite, but that would be uncommon. Also that url doesn't really have a file attached to it unless they uploaded a file named simply 1.
It sounds like they have a problem with their OJS software application. This is a code related problem from what I can see and not a server or hosting issue.
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