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When you guys are adjusting pickup height, what do you in particular listen for?

I've been playing with my Lollar Blackfaces. I haven't been as happy with the sound as I'd hoped, so I've been tweaking them here and there. The closer to the strings that they get, the brighter they sound. The further away, the thinner they sound.

I listen for distinct voices, with combinations having a clearly different voice from the other selections. For me ,it is not about max output but more about useful tones and free vibration in the string. I am also very aware of "wolftones" from the pickup magnets being too close and messing with the string orbit.
Hope that helps.

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How long is that in luthyears?

yeah, if the pups are too high then even if the strings don't rattle against then the magnets can damp thier free movement.

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I presume that you have read what Jason Lollar has to say on the subject:

How close to the strings should I adjust my new Lollar pickups?

That depends a little from pickup to pickup. On a Lollar Vintage Blackface® set or a Lollar Special S Series® we recommend that you start approximately 1/8" from the top of the pickup to the underside of the string (when the string is un fretted). Go a little closer for the high e, and a little further for the low e. On a Lollar Vintage Blonde® or a Lollar Vintage Tweed® you can actually start a bit closer to the strings to begin with. On Lollar T Series pickups 1/8" is also a good starting point. For P-90s, start at around 1/8". Humbuckers work well when you adjust them as close to the strings as possible, without any string interference. Remember, all of these are starting points. The next step is purely up to you. Don't be afraid to adjust pickups closer than you have been told—it won't hurt anything and you may like them as close as they can get and you can always adjust them farther away if you don't like it. Many of our pickups have magnets that are not fully charged in an effort to make them perform more like vintage pickups- with weaker magnets you'll need to raise the pickups closer to get the best dynamic performance. Take time to listen and tweak until you have the pickups set up where they sound best to you.

I usually adjust the tone on the neck pick-up to a tone that I like and then adjust the bridge pick-up so as to get a lightly higher output.

I didn't read that, but they said something similar when I spoke with them a few weeks ago.

These are very clear and articulate pickups, but after playing with them quite a bit, they're too strong willed and want to sound the way they want to sound, tone in my head be damned

I'm going to give some Fralin Blues a shot. I loved them in my telecaster, and I think they had a better voice for modern music. Maybe their strat pickups will, too.

Brett, I like the tip on adjusting until each position has it's own unique voice.

I took this clip to show a seller that the compressor they'd sold me had some issues (the seller was very good and took it back without hesitation), but you can hear the strat with the blackfaces adjusted to an 1/8th inch below the strings. The pickups are clear and articulate, but bright.