Here at MayosMusic, in addition to offering great guitar/bass lessons and complete luthier services that includes guitar and amplifier repairs/restorations, we are also a great resource service. Below is a discussion on the electric guitar/bass pickup height adjustment and a procedure for setting this adjustment.
The final adjustment step for an Electric Guitar/Bass is the "Pick-Up Height Adjustment". This step is often over looked and/or adjusted incorrectly. The most common adjustment error is to set the pick-up height too close to the strings thus causing the pick-up to excerpt what I call a "Magnet Interference Pull" on the strings. This effect causes the string to produce a woobly sound and to NOT PLAY in-tune up and down the fretboard even though the intonation measures correct at the 0-Fret/12th Fret.
Question: Why have players/guitar technicians adjusted the pick-up too close to the strings?
Answer: To get more gain (volume) out of the guitar and thus overdrive an amp for desired crunch and/or distortion sound. However, you sacrifice intonation and playing in tune. A better solution would be to use a "Pre-Amp Gain Pedal" to produce the desired gain needed.
If your guitar is always strung with the same gauge of strings and the adjustments stay the same, then the pick-up height adjustment only needs to be done once.
Also, avoid letting the strings lay on the pick-up when changing strings. This can magnetize the strings and cause the above mentioned problems. A solution is to lay down a barrier such as a piece of foam or rag that keeps the strings away from the Pick-Up during re-stringing.
Tight fitting guitar cases that press the strings down and thus casing them to contact/touch the pick-up can cause the same above mentioned problems. Look at the inside lid of the case for indented marks. Solution: Place a pad (foam) between the strings and the pick-up before closing the case OR get a new case.