Ended up having to move to a new server with a fresh OS. In the process of rebuilding the TV site since the backups had malicious code that I was a bit nervous about restoring. Will be a busy few days here
I know your busy but if you want to guarantee that there is no hanky-panky with your files you can try this method.
- create a sub-folder of your root
- install Clarion responsive RocketLauncher for J3
- in the this dev sub-folder delete all the article content
- get and install this
http://www.eshiol.it/joomla/j2xml/j2xml-3.html
on the real site
- run it to EXPORT all your articles and users to an XML file
- then install it on the dev site and IMPORT all your articles and users from the XML file
This will ensure only CLEAN files will exist on the dev. The only drawback you will have to re-create your module content.
Once you've duplicated the root site you can use Akeeba to clone the dev to the real site.
Thanks for the tip but that site you are referring to never had an issue and I had successfully transferred it to the new server with no issues. I still have some minor issues with the Oculas template that I am working through.