I'll see what I can do to clean and combine those but, comparing them with the previous scans that we had, I'm not sure that the colors look correct? They seem a bit dark (the dotted dark grey parts look plain black, for example).
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.
Since colors are translucent in these, it would be a matter of applying "Multiply" (or similar) blending to the topmost layer, maybe there's some kind of shaders which can do that?
That's how the "COMBINED" images in that folder were made (in Photoshop), for the record.