A bit of light reading including Optimising pickup height:
http://www.musicradar.com/news/guitars/50-steps-to-better-electric-guitar-tone-528489/34/1To get the best out of your guitar, it's important that the pickups are adjusted to the right height. The closer they are to the strings, the louder they will sound, but as always, it's not just a case of louder is better...
Humbuckers
As a rule of thumb, humbuckers can sit as close as you want for the volume you want. To begin, fret the top and bottom E strings at the final fret. Using a steel rule, adjust the humbucker’s height until its treble and bass sides both sit evenly 2.5mm beneath the fretted strings. (sjwebb90 comment - 2.5mm or thereabouts works for me)
Single-coils
Strats should be adjusted to sit with the treble side slightly higher than the bass for a good tonal balance. Fret the two outer strings at the final fret, then adjust the pickups so the polepiece tops sit 2.5mm and 3.5mm from the treble and bass E strings respectively.
(sjwebb90 comment- Having only installed one set of Irish Tours I found they were the same height on both top E and bottom E. I'd be interested in what other single coil BKP users setting were and if they found similar?)
Watch out for wolf notes – these occur when the pickup’s magnetic field is too close to the string’s field of movement, preventing it from vibrating naturally. Step away from the strings, sir!
Balance
Strings vibrate more freely near the neck than they do at the bridge, meaning neck pickups sound louder for a given height – so a little experimentation with relative height settings may be necessary to establish a good balance in volume between pairs or trios of pickups.
Tim Mills of Bare Knuckle Pickups explains: “The signal on the bridge coil is going to be much thinner and brighter because the string’s barely moving. It’s literally just off the saddle and over the coil. By the time you get to the neck pickup, the strings are able to move much more freely.
"These days, modern pickup makers try to allow for that by calibrating the wind as you go from bridge to neck, so hopefully you’re not having to make such an extreme height adjustment between two or three coils.”