Hey Wokka, what if you got a vinyl representation of the fret positions an marker dots computer cut?
You get them to cut it complete with a border down the sides, about 10mm wide of each side of the neck, to hold all of the frets in the right spot. They cut it, lay a wide backing sheet over the top and then you apply in one hit, and trim the "border" off at the neck sides.
You can then just lay clear over the top of it.