Finally I was able to find a way to do exactly what I wanted. Though adding Custom Taxonomy or Custom Post Type can easily be added, while having its Template file, as following:
Appearance> Menus > selecting Links widget > putting link of custom post type or taxonomy http://yourdomain.com/your-custom-post-or-taxonomy
But also this answer help you to have a widget for your custom post type and taxonomy to select from them. The code there is for custom post type, but after working it around, it is now working for me as I had many custom post types and taxonomies.
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