Are yo planning on using a separate fretboard? That would make the idea a lot easier to implement. Then you could chamber the neck and run fiber optic to the side markers, and use a single LED or a multicolor. I would recommend against the front markers, for asthetic reasons, but your guitar, your rules....
"A problem shared is a problem halved; so is this really your problem or half of someone else's? -Ricky Gervais, The Office"