Firestar, here is my thinking on the colors..
Green is easy for the eye to pick up, it is a good contrast against the black...
However, Yellow is an even easier color for the eye to pick up...the contrast of the yellow against green forces your eyes to focus on your front sight.....it is very easy to find, and focus on, even if you arent trying.
As for bondo, that would be great...I probably would have used that if I had thought of it...Just make sure you wipe a nice divot out of it at the top when it is still wet, to allow you room to drip the paint into.
Just be wary of putting a more vibrant color on you rear sights...your eyes will be drawn to it, making front sight focus harder.