How can I run a directive after the dom has finished rendering?

It depends on how your $(‘site-header’) is constructed.

You can try to use $timeout with 0 delay. Something like:

return function(scope, element, attrs) {
    $timeout(function(){
        $('.main').height( $('.site-header').height() -  $('.site-footer').height() );
    });        
}

Explanations how it works: one, two.

Don’t forget to inject $timeout in your directive:

.directive('sticky', function($timeout)