Trouble implementing Jquery + Javascript in footer hook

First off I should point out I'm a javascript/jquery rookie and am trying my best to implement scripts that others have written. I'm currently working on a mock site in my spare time, which I'm basing off an existing site. Im doing this just to build my skills so its completely non-commercial.

Currently I've got a nice scroll reveal script loaded that fades in my content as you scroll. I found that pretty easy to implement, however now I'm trying to load in a script I found here:
https://jsfiddle.net/cse_tushar/Dxtyu/141/
I've added the following to my footer hook in a <script></script> tag:

$(document).ready(function () {
    $(document).on("scroll", onScroll);
    
    //smoothscroll
    $('a[href^="#"]').on('click', function (e) {
        e.preventDefault();
        $(document).off("scroll");
        
        $('a').each(function () {
            $(this).removeClass('active');
        })
        $(this).addClass('active');
      
        var target = this.hash,
            menu = target;
        $target = $(target);
        $('html, body').stop().animate({
            'scrollTop': $target.offset().top+2
        }, 500, 'swing', function () {
            window.location.hash = target;
            $(document).on("scroll", onScroll);
        });
    });
});

function onScroll(event){
    var scrollPos = $(document).scrollTop();
    $('#menu-center a').each(function () {
        var currLink = $(this);
        var refElement = $(currLink.attr("href"));
        if (refElement.position().top <= scrollPos && refElement.position().top + refElement.height() > scrollPos) {
            $('#menu-center ul li a').removeClass("active");
            currLink.addClass("active");
        }
        else{
            currLink.removeClass("active");
        }
    });
}

However nothing happens when I click to scroll the page by my slideout menu anchors.
I understand why the later half of the script doesnt work as I dont have the classes set up properly, but from what I see the smooth scroll should work regardless.

Are you able to lend some assistance, I honestly dont know what I'm doing wrong. I've been trying to troubleshoot the problem for a good 2 hours now, and I'm sure its something really basic that I'm failing to grasp.

Thanks in advance for your help.