There's only so much we can all understand via text with limited sentences where we need the aid of images. In fact, we'd have required both.
Make and model of your motherboard, case and processor you're working with. Include an image to show us how tight it is inside the chassis. You can host the image on Imgur and then parse a link here for us to see.
Ideas can be numerous, the only question is what sort of ideas can you not do(like buy a new case, change the cooler to something different, replace the side panel entirely)?