I don't know that you would necessarily want to use perfectly clear epoxy in this instance. Given that the light source will not be a fiber-optic side-light, but rather one or more end-lights illuminating the fret line from beneath the fret board, it would be much more apparent where the light sources were coming through if the line was perfectly clear. A translucent material would have a more diffusive effect, and help to obfuscate the origin of the light in the fret line.
I am sort of a lighting geek, and have done a fair amount of fiber optic lighting, and the potential for doing cool things to a build are pretty extraordinary now. One idea I had toyed with for a while was building a chambered body with a starfield in the face. Given the fact that the LED light sources are so small and energy efficient now, and you can even get them with twinkle effect in them, it would actually not be that difficult. On something like that you would probably want to use System 3 or other highly flowable epoxy on the face of the instrument post installation as the final finish to protect the fiber ends, as well as securing the fibers. It would only be really dramatic looking in very dark conditions, but when in a dark environment, it would be pretty cool.
