#1) I’d recommend custom fields. When you are creating or editing a page, they appear in Advanced Options directly below the page content editing form.
Each custom field takes a ‘key’ and a ‘value’. This is pretty straight-forward. On the template end I use this to give me a set of variables matching the keys, with values assigned:
<?php foreach (get_post_custom() as $key => $value) { $$key = $value; } ?>
So if you establish a ‘section’ custom-field key that you set for each page, with values matching the 4 (or whatever) different sections of the site requiring different navigation, all you need to do is check the value of $section on each page and load the relevant nav. Does that makes sense?
#2) Check the ‘settings’ tab, and the ‘permalinks’ sub tab. Or, more reliably, on the page creation/editing form a permalink line appears (after you have entered a title), and you can change it as you like.
#3) Good question. I don’t know. I’ve always used posts instead of pages to build a CMS on WP – which makes that much simpler because you just call the loop as many times as you need.