Installing extra/additional plugins for standalone CKEditor module library
Here are the steps about how I am doing it:


install CKEditor using the CKEditor module and NOT through using the wysiwyg module.
Put plugin in sites/all/modules/ckeditor/plugins and NOT in /sites/all/modules/ckeditor/ckeditor/plugins
Go to /admin/config/content/ckeditor and click edit on the profile you're using.
Under Editor Apperance, from Available buttons, drag up your plugin icon to the Current tool bar.




Scroll down a bit and you will see a Plugins section.





Checkmark your plugin and save changes.


PS: Here is my CkEditor Global Profile settings /admin/config/content/ckeditor/edit/