To me it looks like this has been answered, but just in case:
Stock fuel system is fine for stage 3, but apparently not much further.
Adding Contain Flow portion of 2Micron's kits will work fine with stage 3, but it doesn't protect some of the most expensive parts of the fuel system in the event of a pump failure (injectors, rail, FP control solenoid, FP sensor.)
Adding Pure Flow portion brings up the issues JFettig brought up. You'll have problems with stage 3, and sometimes stage 2. These problems include an inability of the car to maintain fuel rail pressure at higher RPMs, leading to lost power, CEL, limp mode, etc. I don't know if it actually damages the engine or fuel system.. I'm suspecting no. All it is throwing a code over is low rail pressure, not -no- rail pressure.