Hey Sam,
Great that you've made an account and have started recreating your project but, alas, I feel you might have already gone overboard.
You don't need all of those elements and libraries to test the functionality you are having issues with. In fact, you want to remove all of it. Like I said before, all you need is a simple box in the 3D environment and scrollTrigger. Nothing else. Then, you can more easily work out what to do.
You stated at the start of the thread that you were having issues making the object scale on scroll so, let's focus on that. Not on loading external models, bootstrap, jQuery, popper and what not. You are not looking to recreate you whole project in Codepen.
So, create a simple scene. One cube, no lights, a basic material, one basic perspective camera, no textures or images, no models, just that. Then, add scrollTrigger to it and see if you can cause the cube to scale when scrolling.