I'll chime in here, if'n y'all don't mind.....
c1 says that adjusting the pickup height is about the last thing a player thinks about, and I believe he's correct on that score. For whatever reason they did that, they were correct - pickup height is the last thing you adjust before it's Miller Time.
Whyzat?
Because as you play with the neck alignment and the bridge saddles (height and length), you constantly change the position of the strings in relation to the pickups themselves. Adjusting the pup heights at this point would be fruitless - indeed, it would just cause more work later on.
So how do I do all this? Pretty simple. Doesn't even need a sticky, nor a whole book.... although I congratulate those authors who can convince a publishing house to throw some dead trees at it.
Start by lowering the pup heights from where they are now. Don't argue with me, just do it. Go down at least two whole screw turns, but go down even more, if you can stand the excitement. There. Now the pup's magnetic fields will have the least interaction with the strings. That's important for two reasons:
1) When you set the string height, the magnetic field will interfere to some extent with what you hear. IOW, the field can actually pull the string out of alignment, thus causing you to hear artifacts that might not be otherwise present. Count 'choking' as you bend a string as one of these artifacts. The overall effect won't be much, not by a long shot, but if you're gonna do this right.....
2) When setting the intonation (the string length), you again risk the magnetic field's pull on the string giving you a false result. Particularly if you use the harmonic method, your results can get all wonky in a heartbeat, if the pickups are stealthily forcing the strings out of whack.
From this, you can see that adjusting your strings comes first, then adjusting your pup heights. So how close should the pups be to the strings, when all else is said and done?
Easy, but time consuming. At a glance, my first-pass effort is to eliminate the dreaded 'Strat-itis' effect. That's where the pickup is so close that it actually forces the string to vibrate in a very unpleasant way. It's actually worse than anything else you can make your guitar do, it just sounds like crap.
So I fret the low-E string at about the 15th fret, and then slowly raise the Neck pup until I hear non-musicality coming from the amp (or the headphones out of some other device - this procedure is not dependent on the amplification chain in order to get it right). Back off a half turn, and make sure that no matter how hard I strike the strings, there's no interference with my Mojo. Go over to the other E string, and repeat. Usually the two sides will 'interact', and need to be balanced between them before I call it good.
Leave the Neck pup in you've just set it, and adjust the Middle pup (if you've got one) to sound as you wish. Of course it can get too close to the strings too, but by now, I'm sure you know how to recognize that symptom, and how to avoid it, right?
But wait, what if the tone of the two pups in combination is not what you want? Then you need to decide which way is more important to you - lowering the Neck to make the magic, or lowering the Middle to avoid the cruft. You can't go higher, right? And there's no real harm in lowering anything, that "maximum" height was only a starting point that we could trust to not give us any grief - it's not cast in concrete!
Lather, rinse and repeat for the Bridge pup, and you're all set.
Well, the procedure is rather simple with only two pups, but with three, it can take some time to balance things out, I admit. You may well end up spending two hours on this, I dunno. In fact, let me make another suggestion here: the moment you start experiencing "Huh?" moments, stop and take a break. Don't try to get it all at one sitting, at least not until you've done this several times. Additionally, take notes at each step. Even now, I occasionally find myself repeating a step or series of steps, just because of CRS. When I finally recognize that moment, I don't just take a break for a few minutes, I put it all up for the night, and come back the next day.... and that's when I really appreciate the notes I took previously! ;D
And when all else fails, get another set of ears. Your bud, your spouse, it won't matter, but not the dog - he's strictly a digital source of information - he tolerates it so he stays, or he hates it so he leaves. Not much middle ground to work with there.
~!~!~!~!~!~!~!~
The Clff Notes version:
1) The chain of amplification devices between the guitar and your ears is not important. You are adjusting for playability without harm to your tone, not tone itself.
2) Adjust your pickups so that they don't cause the strings to crap out on you.
3) You may screw around some more, if you should feel the need to keep playing with it until something breaks.
4) There is no magic here, so ignore the little man behind the curtain.
HTH
sumgai
