This was just supposed to be a comment but has grown too large, but it's not a proper answer:
this is something I'm also working on integrating into a theme at the moment. in your case the easiest/quickest method might be to attach your click call for the wpColorPicker to the same div tag that calls the media-uploader, or you can refer to this Is it possible to listen to a "style change" event? and trigger your colorpicker when the $('#__wp-uploader-id-2')
div's css display 'block' attribute changes.
The second method is to extend the thickbox functionality (the uploader is inside a thickbox) to callback when the uploader is opened.
The third method is to extend the media uploader's js functionality, though I'm not familiar with this.
If it helps, in the long run I found dealing with the colorPickers options and layout controls to be a lot of work (I was using several at once), and in the end found and implemented this: https://acko.net/blog/farbtastic-jquery-color-picker-plug-in/
update: found this from https://wordpress.stackexchange.com/questions/92415/image-upload-callback-in-new-3-5-media which extends the uploader's callback function:
$.extend( wp.Uploader.prototype, {
init : function(){
console.log( 'uploader is initialised' );
$('.color-field').wpColorPicker(); // not sure exactly when it initialises ?
},
success : function(filename){
console.log( 'uploader has loaded: '+ filename );
$('.color-field').wpColorPicker(); // or you might want to add the colorbox once a file is actually uploaded?
},
});
good luck