I need to change the size of the ZoomWindow and make a couple style tweaks (border, cursor, etc..) I see this info is all coming from the /js/lib/elevatezoom js files so do I just edit the non-minified version, then re-minify it? Or is there a more 'proper' way to work with these js files?
The best would be to use css. Assuming you're using default RWD theme as elevate zoom is availiable in RWD theme only (i think :), edit proper classes in scss/module/_catalog-products.scss. those clasess are contained in .product-im-box class. Or edit styles.css (the same classes) if sass is not your thing.