On wire bigger than #6 you only need to identify the ends near the terminations. Be sure you do it before you pull in the wire so you are sure you get the same wire on each end.
Not in NYC you can't. Most inspectors do not accept striping of the wires either. (taping it like a candy cane for example).
I've used a black sharpie to re-identify a white switch leg in a pinch before..., but I've yet to re-identify 500' of anything. I'm just curious GDKNY why you would need to color the entire run? I know NYC has a lot of their own oddities when it comes to code amendments.
We're doing a 3 Phase, 1200A service for a strip of businesses. All the wires from the switches, in the troughs and all the enclosures are visible from end to end. And like you said, its NYC.