Does the distance between the pickups and the strings change to sound of the guitar at all? I'd try it and figure it out but I'm currently out of strings.
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Dont get too close though. My friend has his too close to his pickups and his distortion sounds terrible.
the distance effects the clarity of the sound of each pickup, as well as makes each one stronger/weaker. also the side of the pickup that is closest (treble or bass) will make those frequencies more pronounced.
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experiment. I have a HSS setup and i have my top S the highest, the middle down at the same size of the pickguard, and my humbucker up high. Just mess with it untilly ou find something that you like.
i also have a problem...i play with metal settings..and need the pickup height to agree with it...i think it sounds good, but i havent heard anything else you know?

ok well...i have a string through body, and sometimes my strings actually hit the bridge pup if i rest my hand on the strings...to high?
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yes lower them a bit, to set mine i just keep on playing while lowering them like a half spin of the screw and such untill it sounds perfect
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Do you mean output, because they are essentially different things if want to be actually correct.