This was a long drawn out process. First I was creating the Virtual Servers within Webmin, I did a lot of work to get the php to work i those, but I did it. Then I went to try to set up the email accounts and all of them regardless of domain were showing up as email@example.com and I couldn't receieve mail to the actual firstname.lastname@example.org. So I decided to just create a Virtual Server within Virtualmin and that worked for the email. I am not able to receive email to the email@example.com, but with the settings that Virtualmin put into my httpd.conf file I was unable to connect to the site files. So I made changes to that information and here is my current issue.
I tried setting the DirectoryIndex to just index.php and that doesn't work. I've searched for over 10 hours trying to find someone else with the same issue and I've made changes to my httpd.conf file that I don't even know what it should look like anymore. (Just making changes to the VirtualHost section)
Please let me know what information you need from me to help me fix this.
CentOS 6 on VPS Virtualmin/Webmin/Usermin Apache