I've posted this setup procedure in other's threads in short form before, but here it is in full - and updated (very slightly). This procedure is not meant to be definitive. There are many approaches to setup which are capable of producing excellent results, but I believe that this one is the most efficient. Manufacturers often stipulate "magic" numbers for setup. I don't believe that setup should involve any such numbers. They're reasonable and time-efficient for average, factory settings on stock guitars, but they may not be suitable for you, your playing style and choice of strings. The only tools required here are the hex wrenches for the truss rod and bridge saddle grub screws and nut files. No feeler gauges are required and certainly no crude practices involving business cards and the like are present here. No measurements of any kind are made or are necessary. There is only one simple criterium involved at each stage and that is to be ONLY JUST FREE of fret buzz when you play normally. This setup method will deal automatically with any natural resonances particular to your guitar which can result in some notes being more prone to buzz than others. STRATOCASTER-TYPE VIBRATO SYSTEMS ONLY: If you're setting up a guitar with a Stratocaster-type vibrato, you first need to decide whether you want the system to float or be decked. If decked for flattening only, then tighten the spring tension screws to achieve that snugly with the guitar in tune. If the vibrato is never to be used, then there are several effective methods of hard decking. If it's to float, then you need the bridge plate to be temporarily held firmly in a tilted position. This is most easily done by placing a suitably thick piece of wood between the bottom of the inertia block and the rear part of the routing at the back of the body. Remove a spring so that the piece of wood is held firmly in place when the guitar is in tune. Once the whole setup procedure is finished, the spring can be replaced and the spring tension screws adjusted so that the hold on the piece of wood is only just loosened. Later on in the general setup procedure below, setting the intonation on a floating vibrato Stratocaster will involve unavoidable bridge height adjustments due to the slope of the bridge plate. Also, remember that there are overall bridge saddle height differences between decked and floating positions which can necessitate a change in the amount of neck shimming required. THE GENERAL SETUP PROCEDURE: Assuming that ... 1: The frets are level. 2: The guitar is fitted with your preferred gauge of strings. 3: The guitar is in tune, ... then this setup procedure will result in the very lowest action which is buzz-free everywhere. This may or may not be the final action that you want, but it's a crucial setup waypoint which will eventually benefit everyone. In this setup method, three distinct playing zones of the neck are considered in turn and in such an order to be least dependent on one another. When setting up each zone, make sure that the guitar is in tune and that you play as you normally would - that's important. The first zone to consider is that of the very highest frets. There is ONLY ONE adjustment that can affect playability in this zone and that is bridge saddle height, so adjust the saddles to give a just buzz-free action here. I'm talking about frets roughly from around the 15th on up. The neck in this zone is usually overlapping the body and unaffected by truss rod adjustment. The overall action and the situation at lower positions can be completely ignored at this stage. You need only concern yourself with being just buzz-free at these highest frets. Bridge saddle height adjustments will very likely require you to re-tune, so do that before continuing. The nut slots should then be cut so that there is a barely visible gap between each string and the 1st fret when each string is held down lightly between the 2nd and 3rd frets. If your guitar has a vibrato system, then you may prefer to allow a tiny bit extra for future wear. The next adjustment is that of neck relief. It makes most sense to leave this adjustment until the string heights at the bridge and nut have been set. The truss rod should now be adjusted to give just buzz-free playing from the open strings to around fret 15. The neck profile should not be straight, but slightly concave to follow approximately the envelope shape of fundamental string vibration modes. If you get buzz anywhere in this extensive zone, then loosen the truss rod until it just clears. If the action is completely buzz-free in this zone to begin with, then tighten the rod until you get the very first fret buzz occurrences and then loosen it until the buzz just clears again. My experience is that truss rod effectiveness can vary widely from guitar to guitar, so very fine adjustment can be problematic. Finally, set the intonation on each string to be correct at the 12th fret. Remember that moving a bridge saddle forward or backward will affect the tuning, so make sure that you're always making a valid test on a correctly tuned open string. It's a good idea to set the intonation on the 1st and 6th strings first and then provisionally adjust the bridge saddles for the inner strings to the familiar staggered pattern. This will get you very close and involve less re-tuning when making the final tweaks. At this point your guitar will be set up with the lowest possible buzz-free action. If this action is too low for you, then simply raise the bridge saddles to give the action that you prefer. Whichever action you finally settle on, be assured that you have a setup capable of the widest possible range of actions that are free from fret buzz. With playability dealt with, all that's left now is to adjust pickup heights and/or string balances. Moving a pickup (or polepieces) closer to the strings increases non-linearity (distortion) of the response as well as the output and vice versa. There are no rules, it's just a matter of experimentation and preference.