...
After you have leveled the camera, you should navigate the camera in the viewport only by panning (Alt+MMB) to avoid rotating it up/down and thus creating a three point perspective again. Once you have the view you want, use the Shift Lens parameters to move the frame up/down/left/right. It acts like percentage of the size of your image, so a 100% shift in the Y axis will offset the image up exactly the height of the image.
