WordPress doesn’t Load JQuery Now? Do I need to enqueue JQuery also?

Your issue is that you are trying to use the normal jQuery shortcut ($) which doesn’t work by default as the WordPress version of jQuery is in compatibility mode. You need to wrap the code in your custom.js file in an anonymous function to map jQuery to $ as shown below:

(function($) {

    //Your code here

})( jQuery );

or alternatively, replace all instances of ‘$’ with ‘jQuery’.