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→Fret Buzz
Beyond those adjustments, the only way to get your action lower with the same amount of buzz is to have the frets re-leveled or the nut filed down. I would get a professional to do such modifications, although there are plenty of tutorials on the web that can help you. I'd try to find several of them, as some may make them sound way easier than they are. Filing and/or replacing your nut is the far simpler of the two, but you'll need precise tools to do it at a professional level.
== Intonation ==
Intonation is basically how in tune the guitar is at different frets and strings. If a guitar is intonated poorly, it will sound out of tune when playing notes higher on the fretboard. Chords will be notably dissonant when they shouldn't be.
Most people don't pay much attention to intonation, yet it is absolutely crucial to sound good, especially in a band or recording environment. It's also a fairly simple and risk-free adjustment, although it may take a little time.
The easiest way to intonate the guitar is by comparing the pitch of the 12th fret harmonic vs. the fretted note. If the fretted note is sharper than the harmonic, the string must be lengthened, which usually involves moving the individual bridge saddle away from the nut. If it is flatter, then the string must be shortened by moving the saddle closer to the nut. Once all your strings are intonated, tune up your guitar. You'll notice it will sound much better across the fretboard, especially for chords.
Note that intonation is also dependent on the rest of your setup, particularly your action. If you have a high action, you have to press the string down a significant distance to fret it, which is adding tension (and possibly length) to the string. This is why it is difficult to intonate a guitar with high action. You can match the 12th harmonic to the 12th fretted note, but other spots on the fretboard may not be consistently in tune. The same principle applies to a guitar with a high nut height. You have to exert more tension on the frets close to the nut to properly fret them, causing them to be sharper than other areas of the neck.
Thus, I like to intonate using at least 2-3 comparisons. I'll start with the 12th harmonic vs 12th fret, then I'll try the 7th fret vs. 19th fret. If that's off, maybe I need to lower my action a little. Then I'll try the 2nd fret vs. 14th. If there's a discrepancy there, it tells me how much impact my nut height is having on getting a proper intonation. If I can't get all of these 3 tests perfect, I'll compromise and get all 3 as close as possible rather than have one perfect and the other 2 way off.
Keep in mind that lower quality instruments might have issues with the nut or possibly even with the fret spacing. Unlevel frets can also throw off intonation, making it impossible to intonate. Technically, perfect intonation is impossible - the best you can do is a compromise to get all the notes as close to in-tune as possible.
== Pickup Height ==
===Passives===
Too low and you lose SNR and your dynamic response gets messed up, too high and you get input clipping on your device, as well as "pole pull", which can screw up your intonation and kill sustain. I recommend allowing them to have a safe distance. Also, don't confuse output level with SNR. Raising your pickups will increase their output level, but it is probably not improving their SNR unless they were very low (or extremely weak) to start.
===Actives===
EMG recommends you to put them as close as possible. I followed this advice when I had these pickups and never noticed any problems with doing so. For the Blackouts, this is where things get a little interesting. The pickups seem to have some kind of buffer, so they will not output above a certain level. So it's like a limiter effect. If you raise them close, you will actually reduce the dynamics to your attack. I prefer to keep a medium distance on these pickups. They work pretty well at a distance. I actually have them as low as possible on my custom Jem (which actually isn’t THAT low). Even with some distance, they still have a higher-than-normal output. But if you go too low, you’ll notice you can’t get good artificial harmonics or softer notes to sound good.
== Bridge ==
I can't tell you much about how this type of bridge material will affect your tone, but I do know that a fixed bridge will best maximize your frequency response and sustain. If you have a floating bridge, you may lose a little brightness (or some thickness) - something to keep in mind for pickup selection and tone editing. You can use a Tremel-no or put a block of wood under the bridge to keep it from floating. I recommend the Tremel-no – it allows you to switch on the fly by turning a thumb-screw.
Also, if you have a Stat type bridge (whammy dives only) or floating bridge, I recommend stuffing the bear claw cavity in the back of the guitar with Kleenex or cotton balls or gauze. This will keep the springs from making any noise, so that they do not ring after you play a note. This is essential for hard rock and metal, where you use lots of compression/distortion and have to play punchy rhythm or lead sections that require you to quickly mute all the strings. This is a common technique, not some ill-thought-out hack. Similarly, mute the strings between the nut and tuners to prevent them from ringing. I like to use sticky-tack (earthquake putty), but you can also use foam or a wristband.
== Nut ==
The nut is an often overlooked area of the guitar. It needs to be positioned properly for the guitar to intonate correctly. It has a strong affect on the action. An improperly filed nut can cause tuning and sustain issues or cause buzzing/ringing on open strings. I recommend having a professional adjust your nut. To file it correctly it is best done with specialized filing tools, which are too costly to justify a one-time use. I like my nut to be like the 0th fret - providing a similar clearance over the 1st fret for open strings as they have over the 2nd fret when fretting the 1st fret. Any lower and they'll buzz. Any higher and intonation is off and action is unnecessarily high. The strings should make firm contact with the nut right where they leave the nut and travel over the fretboard. The grooves should point directly towards the tuning pegs. They should be wide enough to fit the string in easily and so that it doesn't pinch when tuning or bending. It also has to be smooth so the string slides easily over it and doesn't break. But it can't be so wide as to allow the string to rattle in the groove. They have to be deep enough so the strings don't pop out, but shallow enough so the strings can easily fit into and out of the nut.
The simplest and easiest tweak to help fix a nut is to ''draw in the grooves'' with a pencil. The graphite will lubricate the string's movement in the groove, so it doesn't pinch. This helps keep your strings in tune better.