It can be complicated getting jquery plugins working. I think the biggest issue is that your plugin scripts are loaded before the main jquery scripts and they need to come in after.
I would create a custom usercontrol and put it in the layout.master just inside the <form>
Inside the UserControl you can add the plugin script using something like this from code but changing the path and the key to reflect your scripts.
"custompluginname", "\n<script src=\""
This should make it load your scripts below the main jquery scripts.
Hope it helps,