There are also tinted primers available for pre-treating the ends of PVC prior to gluing joints. I know I have seen pink, purple and yellow, I don't see a reason why it cannot be used for color coding. Just use it outside! Most of that stuff is noxious as heck. There is also a company called Dykem which makes layout marking fluids. I've used them a lot, mostly on metals prior to precision scribing on surface plates. It comes in a rainbow of colors (even white), and if they stick to bare metal, I'd imagine they'd hold to plastic well enough. Alcohol cleans it off pretty quick.
On another tack, automotive plastic bumper paint should be the cat's meow for painting plastic subjected to flexing. . .might be cheaper by the quart than other options.
I have discovered the ultimate question to life the universe and everything. "Does it burn?"