How do you solve script library conflicts?

I took over a web project and there are many libraries used. JQuery, javascript, bootstrap, d3 to name a few.

I'm running into some IE issues as the site is supposed to be optimized for Chrome and IE. One notable and big issue for the client is that the "back to the top" button is not working in IE and I can't figure out why. I've used several different techniques and they all work standalone, but not in my environment. My question is how can I properly solve this issue. I know it's not a browser issue because the "back to the top" works fine in IE standalone. Is there an easy solution to this? where do I start?

Here is a list of the js libraries being used:

    <script src="assets/js/jquery-3.3.1.min.js"></script>
    <script src="assets/js/application_old.js"></script>
    <script src="assets/js/highstock.src.js"></script>
    <script src="assets/js/exporting.js"></script>
    <script src="assets/js/export-data.js"></script>
    <script src="assets/js/bootstrap.min.js"></script>
    <script src="assets/js/jquery.easing.min.js"></script>
    <script src="assets/js/jquery.mCustomScrollbar.min.js"></script>
    <script src="assets/js/TweenMax.min.js"></script>
    <script src="assets/js/jquery.animateSprite.min.js"></script>        
    <script src="assets/js/jquery.gsap.sprite.js"></script>
    <script src="assets/js/d3.v4.min.js"></script>
    <script src="assets/js/d3-array.v1.min.js"></script>
    <script src="assets/js/d3-collection.v1.min.js"></script>
    <script src="assets/js//d3-color.v1.min.js"></script>
    <script src="assets/js/d3-format.v1.min.js"></script>
    <script src="assets/js/d3-interpolate.v1.min.js"></script>
    <script src="assets/js/d3-time.v1.min.js"></script>
    <script src="assets/js/d3-time-format.v2.min.js"></script>
    <script src="assets/js/d3-scale.v2.min.js"></script>
    <script src="assets/js/d3-tip_0.9.js"></script> 
    <script src="assets/js/selectize.min.js"></script>