I figured I might as well look it up...
Setting the pickup height
After adjusting the action and string height, it's a good idea to adjust the height of the pickups. If the pickups are too close to the strings, the magnetic field can affect the intonation, especially with single coil pickups, as well as cause undesirable distortion. In addition, a pickup that's too close to the strings can kill your sustain since the strong magnetic field will cause the string to stop vibrating prematurely.
Always check the height of the pickup while fretting the string at the highest (last) fret. Measure from the top of the pickup to the bottom of the string. You can also use the pickup height adjustment to balance the the volume and tone of your pickups. For example, if there's too much bottom end, you can lower the bass side of the pickup a bit more to lessen the low end. If you have too much treble, you can lower the treble side, you need to experiment to find the perfect setting.
If you set both pickups to the exact same height, the neck pickup will almost always be louder than the bridge pickup. You can balance this by setting the neck pickup a little lower than the bridge pickup. Also, when you have both pickups selected simultaneously, you can adjust the tone by changing the heights of the two pickups so that the mix is more balanced. What it really comes down to is personal preference in tone and output.
The specs put forth by the manufacturers are merely starting points to depart from, they're not ironclad settings. If you have humbucking pickups with adjustable pole pieces as well - six adjustable screws on top of the pickup, then you can make fine adjustments for individual strings by tweaking the corresponding screw for a given string. This is a good way to balance out individual string volumes. You should start with all pole pieces screwed down flat against the pickup, and make necessary adjustments from there.
Considerations for Single Coil pickups:
If you are working on single coil pickups, you need to keep the heights lower than humbuckers because the magnets are typically much stronger. Prior to beginning a setup, make sure that the pickups are not too close to the strings, or you'll get misleading string buzzes, and intonation problems. The magnets influence is much stronger on the bass side of the pickup due to the mass of the bass strings, so in general, the bass side of the pickup should be lower than the treble side. It will take some experimentation to arrive at the perfect balance of tone and volume, while still maintaining accurate intonation. Remember, the strong magnets used in single coil pickups can cause sharp intonation if they are positioned too close to the strings.
After you make adjustments, check the tone of your guitar each time, and keep fine tuning it. It may take a while before you arrive at the perfect mix for your preference, but it is achievable. If you get a harsh type of distortion from your guitar, try lowering the pickups a bit to yield a creamier, more natural type of distortion. The key here is to experiment.
Specifics for Gibson Guitars
Neck Pickup Bridge Pickup:
- 3/32" on bass and treble side 1/16" on bass and treble side
Specifics for Fender Guitars
Pickup Height Bass side Treble Side:
- Texas specials 8/64" 6/64"
Vintage Style 6/64" 5/64"
Amer/Mex Std 5/65" 4/64"
Humbuckers 4/64" 4/64"
Lace Sensors As close as desired, allowing for string vibration