HWK2:
If an instrument has more than one problem and you only make one correction to the set up, the problem that you are trying to correct can become a compounded problem.
What I'm trying to say is that you can't correct a buzz properly that's being caused by a low nut by raising the bridge saddles. Sometimes making the wrong adjustment will affect the problem leading one to believe that they are on the right track when, in reality, you now have an instrument with 2 problems. I.E., a bad nut AND a mis adjusted saddle. The problem gets a little better but it's still not quite right so the truss rod gets a little tweak or two. Now you have an instrument with 3 problems. A bad nut, a misadjusted saddle and the relief in the neck is wrong. Now you start getting new problems that have nothing to do with the original problem. When the relief was adjusted (misadjusted) the intonation changed so the obvious thing to do is adjust the compensation screws on the bridge. Now you have an instrument that has 4 problems. The original problem (bad nut) plus 3 more problems.
The very first step in a setup is a diagnosis of the setup. The very first adjustment that is made by the "guess and hope" method is the first step down the path of futility.
These are the steps that I use for a complete set up. They are listed in the order that each should be made.
1- Check the relief in the neck and correct if needed.
2- check the nut for correct height. either replace the nut, shim the nut or fill the notches and recut them to the proper depth and width if there is a problem.
3- check the tilt or neck angle. Correct if needed. Unless someone has misadjusted the neck angle, it will rarely need readjustment after the initial set up is made at the factory. Any time the neck has been removed and replaced this adjustment should be checked very carefully. Sometimes a neck will not bed into the pocket in exactly the same position as it was before removal. This step, of course only applies to a bolt on neck instrument.
These first three steps will insure that the instrument is mechanically correct and all other adjustments will be within a correctable range. Once these these adjustments are correct they shouldn't need adjustment again for a long time. The one exception would be the relief which can change slightly with humidity and temp changes.
Just in passing, I know that there are proponents of the zero relief or flat board method of set up. My thoughts on a flat board set up are that a neck can change VERY slightly in the direction that increases back bow resulting in buzz and string rattle. A neck with relief can change slightly with little or no ill effect.
Move on to step 4 only after the first 3 steps are satisfactory.
4- set the string height to your preference with the bridge saddle adjusters.
5- using a rule set the initial string length. Measure from the nut to the octave fret. Adjust the highest pitched string(G on a 4 string) to a length that is double the distance from nut to octave. Adjust the D,A and E shorter by the diameter of the string. These are only rough-in adjustments at this point.
6- using a good stable electronic tuner adjust the compensation for proper intonation. Don't forget to set the tone control on passive basses to zero. You'll find that the tuner is lots more stable with the tone control at zero.
7- Adjust pup height.
I intentionally did not include fret dressing because that is a job for a luthier.
A good rule of thumb is that a buzz problem in the first 4 or 5 frets (closest to nut) are usually nut related. A problem that occurs everywhere on the neck is a neck problem. A problem that occurs only on the higher frets is usually bridge related.
Remember that most of the steps that I listed wont have to be made on every set up but they should always be checked.
Apologies for being long winded.
) I have not had to touch any of the settings, and it plays like a charm with low action, even though I sometimes get a slight buzz on the 1 or 2 frets when my finger slips between the pickups, but I normally play right over the bridge pickup, so no problem (by which I mean if I slip with my finger and catch too much of the string when I pluck). My P-bass on the other hand is a piece of crap. I have to have the action set to like ONE FULL CENTIMETER off the fretboard, by adjusting the bridge, and on top of that, I have had to place stips of paper under the nut, becuase the damn thing leaves my E and !A! string resting on top of my 1st fret. No matter how light I touch the string, it buzzes... So my p-bass has now been adjusted again (finally found that damned alan wrench) and the bridge is WAY down now, but I have to leave the paper under the nut, or I still buzz. My strings start high off the board, and get lower as they go.. or else I buzz to death..Any ideas? 
) and I will make sure that the nut is big enough to take some BIG BOOMERS.. I want at least one bass for some funk/jazz with more punch than Mike Tyson 
