Add class name of content, Hypernate doesn’t work to IE and Chrome

While inserting js directly in header.phpcan work it’s not recommanded to do that. You’d better add your scripts to the WordPress queue:

function wpse_109879_insert_hyphenator() {
 wp_register_script('hyphenator', 'https://raw.github.com/bramstein/hypher/master/dist/jquery.hypher.js', array('jquery'), null , false);
 wp_enqueue_script('hyphenator');
}

add_action('wp_enqueue_scripts','wpse_109879_insert_hyphenator');

Regarding CSS you probably use the wrong class, you can try .single-post or .single

EDIT: I see you use raw script. Maybe you’d better copy paste code from github into another js file you can call directly from your theme. This would allow to insert code you use to initialize hyphenator so you have only one file to manage hyphenator.