Ok, here's what I did that seemed the best:
For I. and II. to avoid using so many ../../../../ in all the src="" and href="" I just settled and used site-relative file references with leading slashes, such as "/includes/menu.php" which would get me to the site root, building the file's location from there.
For the global file reference, BOTH of these worked:
<?php
require_once $_SERVER['DOCUMENT_ROOT'] . "/includes/";
?>
// in `<head>` section
And using <?php include ('menu.php'); ?>
OR THIS ONE WORKED TOO:
<?php
define('ROOT',$_SERVER['DOCUMENT_ROOT']);
define('INCLUDES',ROOT.'/includes/');
?>
// in `<head>` section
And using <?php include (INCLUDES.'menu.php'); ?>
in a file at another level.