I know it's been months since you asked for this but I struggled with the exact same thing, and finally found a solution.
What works for me is to append an empty <div>
to your body
using jQuery and then printing a <style>
tag inside it everytime you change your color, like so:
function changeHoverColor(){
/*
check if your '#custom-css' div exists on page
if not then create it and append it to the body
*/
if( $('#custom-css').length < 1 ){
var $cssDiv = $('<div id="custom-css">');
$cssDiv.appendTo('body');
}
var myColor = '#ff7700'; //change this to your color
/* change the below css to fit your needs */
var myStyle = '<style>a:hover{color:'+myColor+';}</style>';
/*
finally print it inside your div.
Now, every time you pick a color, your new css will be generated and will
overwrite the previous one inside the '#custom-css' div
*/
$('#custom-css').html(myStyle);
}
Hope it helps. Cheers