Can you also do a scan with them stacked? It'll probably end up better than with an image editor. See "COMBINED" ones here: https://mega.nz/#F!uFYSzK7S!U-lJon9jsqyoCX_3y7_KLA!PUgHiA6A (that's the one with the misaligned layer btw, the blue dots on the bottom screen).
In reality, the LCD sheet is in between the 2 layers? It's possible to do it that way in MAME too, but would need a lot of image editing to make the upper layer look nice, alpha blended.
