Just to answer your first question, you want to modify the ViewTemplate in your TiddlyWiki that has the plugin. (screenshot below)
Also, after you've edited the plugin, you have to make sure to save and reload the TiddlyWiki for the change to take effect.
I just tested this again, and it all works A-1. Double-clicking on any tiddler just opens that one tiddler for edit. Double-clicking on either a shadow or a system tiddler does nothing.
Just as a sanity check, download an empty TiddlyWiki, install the plugin in that TiddlyWiki, and see if things work correctly there.
I suspect you made a change to the plugin's javascript and also made this edit I suggest to the ViewTemplate.
If you did change the javascript, you should probably remove the plugin and reinstall.