Ok, use the “Header” link to upload your logo, not any other links. Also, if your logo size is exactly the same size as what is in your functions file then WP won’t need to crop it. If the crop screen shows up, that means the sizes don’t match. So try and reupload the image again on the “Header” link under Appearance….not the “Custom Header” and see if that works, because that’s exactly how most of us do it when adding a logo.
I create awesome sites for awesome people! Contact me if interested – ericsanchez1585@gmail.com