I believe you need to refresh the thumbnails since you changed them in the woocommerce settings. You can do this easily with this plugin.
http://wordpress.org/plugins/regenerate-thumbnails/
As far as leaving them uncropped and changing the size, just do this in a image editor. Otherwise there are several ways to do it. You can do it in the code which handles the image size or by changing the max width and max height in your css for that specific class.
Hope that helps.