Here's "the horse's mouth" on strat setup. I tend to back the pickups on my strat off a bit from this guide, but it's a good starting point.

http://www.fender.com/support/stratocaster.php

Trev, it's always the G, isn't it? It's usually been the angle of the nut slot for me. A pro setup has usually got rid of it. I admit defeat when it comes to cutting nuts accurately and tend to get plastic nuts replaced with bone or one of the better composites.