Almost did it.
I deactivated the plugin in Wordpress admin and then at the bottom of functions.php added:
// Include the plugin.php file so you have access to the activate_plugin() function
require_once(ABSPATH .'/wp-admin/includes/plugin.php');
// Activate your plugin
activate_plugin(ABSPATH .'/wp-content/plugins/ad-inserter/ad-inserter.php');
which I read about here: http://wordpress.stackexchange.com/questions/4041/how-to-activate-plugins-via-code
But it then activated it globally.....