magnetizing a strat pickup with powerful rare-earth magnets
With all the talk out there about scatterwinding and coil wire types, it's easy to forget about how much of a role the magnets play on the sound of the pickup. A lot of pickup manufacturers will charge the poles all the way up and be done with it giving little thought to "tuning" the magnets, but a few of the boutique builders out there will take the time to "hand weaken" the magnets.
To charge up the poles, rare-earth mangets, like those used in guitar repair, are placed in the jaws of a vice. One has it's north pole facing in and the other south. The rare-earth magnets will charge the Alnico poles with the opposite charge, north charges south and south charges north. This is because we all know that if you put two magnets with a south polarity in close proximity, they will repel or demagnetize each-other. As the bobbin with the magnets is swiped between the rare-earth magnets, it is fully charged to about 35 gauss.
A fully-charged south-up Strat pickup
Now that the pole is charged all the way up, we can widen the jaws of the vice to about twice as far as they were before. The pickup is flipped around so that it's south pole will be facing the south pole of the rare-earth magnets and north will be facing north. With the jaws of the vice farther apart, we are just weakening the magnets a little bit, the closer we move the jaws of the vice, the more magnetism we are removing. It only takes two or three swipes through through the jaws to weaken the poles a little bit. In general, I weaken my neck pickups to less than 30 gauss and my bridge pickups to less than 20 gauss.
By weakening the magnets, we are essentially aging the pickups to sound like something 40 or 50 years old.
Setting pickup height
Depress the first and sixth strings at the last fret. Now with a ruler measure from the bottom of the string to the top of the pole. In general, bridge single coils should be about 1/8" away from the strings. Humbuckers can be set a little closer. The closer the pickup is to the string, the more bright or harsh the tone will be, the farther away it is the warmer the tone. Once you get something you are happy with you can move on to the neck pickup. Since the strings are vibrating farther over the neck pickup, this pickup will always be louder and warmer than the bridge pickup. Lower the neck pickup towards the body until the volume is even with the bridge pickup.
It's really a matter of personal taste and there is no wrong way to set magnetism or pickup height, but if the pickup is too close to the string it will pull on it too hard, killing your sustain and messing with intonation. If the pickup is too far away it will sound too dark and quiet.