If you are unsuccessful in maintaining registration at the scanning level, rotating the scans in Photoshop will be necessary to ensure precise registration. Turn down the opacity of the top layer to check registration. If the two images are out of register, the image looks like it is suffering from double vision. As the two images get closer in register, the composite will look slightly out of focus. When precise registration is achieved, the image will appear sharp.
Critical focus is a matter of one or two pixels.
You can activate the move tool and use the arrow keys to nudge the images into alignment for precise registration. Don't forget to zoom in during this process. Add layer masks to hide less desirable information. The bottom layer needs no mask. Select and fill large areas.