Where to upload my new custom ShortCode in Separate .php file?

In general, special theme functionality (including shortcodes) should be placed in your theme’s functions.php file, which is in the root of your theme folder. If the code is less than a few dozen lines, it probably won’t be worth creating a separate file (unless you just really want to organize your code that way).

So the shortcode functionality and the add_shortcode() call should be in functions.php.

Let’s say you do want to separate it though. You can include your myShortCodes.php file like this in your functions.php file:

require_once('myShortCodes.php');

And then you can have the code (including the add_shortcode() call) kept in myShortCodes.php.

It’s recommended to not alter the WordPress core files (like wp-includes/shortcodes.php) or put anything in the wp-includes folder because then it’s outside of your theme folder and any upgrades to the WP core will cause your changes to be lost.