Before you even turn a screw on your guitar, you should gather all tools and materials needed. You will need: small screwdrivers in Phillips (no 1) and flat blade varieties, a socket wrench or Allen wrench in the correct size to fit your particular guitar model for neck adjustment, a small 6" ruler with 1/64" increments and a large flat blade screwdriver to adjust the stop bar height if you have a Gibson style guitar. You will also need a fresh set of strings in the gauge of your choice.
If your guitar is really dirty, now would be a good time to clean it with guitar cleaner/polish. The fingerboard should be cleaned with naphtha (lighter fluid), and #0000 steel wool. If you clean the fingerboard, you should treat the wood with lemon oil to keep it from being too dry. Now it's time to install the new strings, stretch them out, and tune the guitar to standard pitch. Notice I didn't include a straight edge in the tool list, that's because you can use one of the strings for that purpose.
We will begin our adjustments with the neck relief because if the neck isn't correct none of the following setup steps can be done. Fret the low E string at the first fret with your left hand (if you're right handed), and at the same time fret the same string at the twelfth fret with your right hand Thumb. While holding these two positions, reach your index finger of your right hand to the center point of the string and press down. You should have the slightest amount of clearance between the string and the middle fret. If not, back off the neck adjusting nut until you have this small amount of clearance. This will allow you to bend strings without fret buzzes. If on the other hand, there is too much clearance, tighten the adjusting nut 1/4 turn at a time until you have that very slight clearance. Your neck is now adjusted properly and we can proceed with the rest of the set up.
Now, place your small ruler on its end on the twelfth fret, beside the high E string. Adjust the bridge height adjusting screw on the treble side until the ruler reads 3/64" between the bottom of the high E string and the top of the twelfth fret. Repeat this process for the low E string, except set the gap at 5/64". Now the string height or "action" is correct. This is the correct method to set up a Gibson style bridge. If your guitar is a Fender style, with individual string saddles, set up the high E saddle for the 3/64" measurement, and increase it a little as you adjust each saddle across the strings, ending up with 5/64" for the low E saddle, with a smooth curve across the string set.
Now we can set the intonation, so the guitar plays in tune with itself for the entire fingerboard. If you have an electronic tuner, plug the guitar into it and it will make this step much easier and more accurate. With the high E string in tune, fret it at the twelfth fret. Is the octave note sharp in relation to the open string? If so, adjust the string length screw to make the string speaking length slightly longer, until the two notes are in tune with themselves. If the higher note is flatter than the open pitch, adjust the screw to make the string length shorter until the notes match. Repeat this process for all six strings.
Now we are ready to adjust the pickups for best tone and even volume for all six strings. Pickup adjustments are not written in stone and are to a degree a matter of preference. The pickups on the low E side should be adjusted further from the strings than the treble side for the most even volume and to prevent the magnets in the pickups from pulling too much on the strings and causing wolf tones and false harmonics. Begin by fretting the high E string at the last fret and adjust the treble side of the pickup to where it is not quite touching the string. Now repeat this on the low E side, but adjust the pickup slightly lower than the treble side. Perform this procedure for each pickup if there is more than one. Plug the guitar into a suitable amp and play while switching through all pickup positions. If the rhythm pickup seems to overpower the lead pickup, back off the adjusting screws on it slightly to improve the pickup volume balance.
Now enjoy playing your guitar knowing it plays its best and very possibly sounds better than you've ever heard it!
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