@pitaj I am not sure whether you intend to incorporate the functionality for adjusting the original navigation item or not. I made some change to your plugin and send you the pull-request
The basic idea behind the change is that I remove the original render logic from menu.tpl and all the navigation is actually rendering through the plugin right now. I remained the admin render logic since it request extra checking logic, which I am not sure how to get via plugin yet. So if the user activate the plugin, it won't render any navigation item before user set it up. In case user do want to revise from the default setting, I provided an extra button within the plugin page called "reset to default", so it will reset the navigation items to the original menu.tpl one.
See if you like it.