Is there is a way to group a large number of WordPress Multisites For Easier Organisation?

One way to do this is using multiple networks. A network is a group of multisites, a new level in the hierarchy.

There is by default no interface for that, you have to use a plugin. My recommendation is WP Multi Network by John James Jacoby, the developer who brought this feature to the WordPress core. The instructions are on the plugin page, and there’s a more elaborate article on wpmudev.

For a list of sites, you have to run a custom database query on the table blogs. I guess there is already something like that in the plugin code that you can use.

However that doesn’t deal with multiple levels, like Country/State/District, so you have to indicate the hierarchy by URLs and use that in your custom listing function, or you write a completely new database table to handle the hierarchies.