Well after thinking a lot about this, I’ve ended up using jQuery to solve my problem whereby it alters the links itself. This can at least give me the option of having a manual navigation using WP Menus.
I think what I’m shooting for is overly complex but it would be good to know if what I’m asking for is feasible in terms of auto-populating a menu.
FYI I used this bit of code to dynamically alter the menu links:
// Alter the links in the navigation so that the page doesn't reload
$(".nav a[href*='" + window.location.pathname + "#']").map(function(){
var currentsection = this.href.split('/').pop();
this.href = currentsection;
});
