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Rex_Rocker , I like my pickups close to the strings.
If using a Floyd Rose guitar, I pull the strings sharp 100%. I raise up the bridge pickup until it touches the taunt strings, then back it down slightly so the strings have clearance over the bridge pickup even when pulled fully sharp.
For the neck pickup, I fret at the 22nd/24th fret on each string and raise the neck pickup until it touches the strings, then back it down slightly so the strings can clear the neck pickup when the highest notes are being played. The pickup remains as close as possible to the strings.
Basically I put the guitar in situations where the strings are closest to the pickups, then back down just slightly from there to give the strings room to move. I have maybe a dime's width when the strings are close to the pickups and maybe a nickel's width or two when at normal tension.
I then tweak from there regarding tone, string balance, volume evenness between pickups, etc.
I am used to dealing with weaker magnets like EMGs. Higher output pickups with stronger magnets might be backed into the body a bit more. A JB would definitely be a pickup I would back into the body more to offset its output, mid spike, and loose low end. A Gibson 500T is another pickup I adjust pretty low because the magnets are so strong on that pickup that they pull your soldering iron during installation (using Triple Shots here).
Also I seem to remember backing an Alternative 8 into the bridge as far as possible many years ago and still not liking it. It always felt too hot, fizzy, and close to the strings. If it's boomy or boxy sounding I back it down. I tend to adjust close because I tend to prefer EMGs, Blackouts, Full Shreds, Parallel Axis Original Trembuckers, and similar pickups that don't have super strong magnets.
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Aceman may disagree on pickups close to the strings, I think. Strong magnets can pull on the strings and deaden sustain. He brought this to my attention and it is a valid argument.
For me the strings near the bridge aren't going to move that much anyway. Often the neck has to be raised to better match the bridge.
It's really all about personal taste and even how much you dig in with the pick, as continually scraping it on the pickups can be annoying.