IMHO, I wouldn't waste my time with setting up PEC manually. At the very least used a web cam and guiding software to record PEC. This is far more accurate than the eye/human reaction time.
If you're serious about establishing the lowest PE possible, get yourself a copy of
ASCOM and
PEMPro. Vixen SkySensor is supported in ASCOM. Download a copy of the new PEMPro 2.0 beta (I think build 28 is the latest). This now supports common web cams, so you don't need a dedicated CCD camera.