I'm trying to figure out where I can learn/figure out where in the js files I actually edit say the width height, x and y of an item scenes. It would be the scenes.js I figured, but I'm not seeing any numbers or anything that can be adjusted.
This can be a little confusing. A scene is just a collection of windows. Those individual windows are defined in the rmmz_windows file.
So if you open up the _scenes file and look for, say, the Scene_Item section for the item screen. You'll see the second function is the create() method and it creates a help window, category window, item window, and actor window.
You can then scroll down to those
methods to see exactly what kind of window each one is. For example, inside createCategoryWindow(), you'll see it's a new Window_ItemCategory. You can then open up your _windows file and search for that to find the specs and functionality for that portion of the item scene.
Back in the scene file, a few lines up, you see a shape (rect = rectangle) is determined by categoryWindowRect(), so you can look at the very next function down to see how the dimensions of that window rectangle are calculated.