Re: How to intonate a strat
Your pickups might be too close to the strings, and if they are, then the magnetic polepieces will pull the strings out of tune - especially the wound strings. Try adjusting the neck and middle pickups far away from the strings for now and then try setting the intonation of the individual bridge pieces again. When you get it so it'll play in tune, then adjust the pickups closer to the strings again. Fret up high on the low E and see if the pickups are pulling it out of tune again. If so, adjust the neck and middle pickups further away from the strings until they don't pull the three wound strings out of tune when you fret them up high on the neck. If you don't use your middle pickup by itself, but only in combination with the neck or bridge pickup, you can adjust it further from the strings than the neck pickup. I've found that the bridge pickup can be adjusted closer to the strings than the other two pickups.