@ALF

My plugins can not be enabled or Disabled individually via the administration page.

Read http://learn.elgg.org/en/stable/appendix/faqs.html#plugin-cannot-start-and-has-been-deactivated-or-this-plugin-is-invalid

I had my site url to be "https://www.mysite.com" is this incorrect?

This is an issue of the server's configuration (e.g. hostname) bcz 'site url' must be like as link to your website not IP

ISSUE FIXED:

This is an issue of the server's configuration (e.g. hostname) bcz 'site url' must be like as link to your website not IP

This Was correct! Switching my Virtual host settings fixed all of my issues! 

<VirtualHost *:80>
    # This is the name of the vhost.
    ServerName www.mysitename.com
    # These are alternative names for this same vhost.
    # We put the other domains here. They will all go to the same place.
    ServerAlias www.mysitename.com
    # Directory where the website code lives.
    DocumentRoot /var/www/html

</VirtualHost>

i returned my site url to there original settings as well
Administration page>Configure>Settings>Advanced Settings, and changed to "https://mydomain.com "

my permmissions to /var/www/html/mod are recursively  // 777 www-data:www-data

Never set the permissions this high, even on a local test site. 644 is more than enough (or it should be)