Changing border colors
Not sure if this is what you're referring to but I prefer a more distinct border around icons in Safari and found this works for me in Yosemite.

System prefs>Accessibility>select "Increase contrast" &amp; set Display contrast to Normal.
(note that this selection automatically selects "Reduce transparency)

While this does not change color,it does distinguish the icon borders.
Makes it easier on my old eyes!