First of all, great idea and take on this set! I love the theme on this, and am very much a fan. I guess you may have considered, but I hope to give some suggestions!
1) Have you considered a custom gray- slightly lighter I think, to match the actual classic dualshock?
2) As for the mods, this is an idea from a friend, @magicpretzel - how about making the mods the dark gray color (like on the d-pad, analog sticks) and maintain the colored legends, just like on the original dualshock.
3) Text mods/Icon + text to further highlight the accent colors? (Very subjective, I know..)
4) Like others have mentioned, I think novelties would really make this set shine.
Excited to see the progress on this!