Yeah man, I agree don't touch the truss rod yet.
The easiest way to see if the truss rod is right is to put your eyes level with the headstock and look down towards the bridge....
The easiest do what I just said, is to set the guitar butt down on a chair, and hold the neck, kind of rock it back and look at it like you'd look at a 2" x 4"..... If it's not bowing up or down a whole lot, I just leave it alone.
Over tightening a truss rod and be a serious problem..... a problem that can lead to permanent warping.
Ok now about your string saddles..... have no fear man, I'll help you the best I can. What you're going to want to do is detune your guitar a little bit.
Ddon't take the string off or anything crazy like that.... you just want to get some of the tension off of them, that's all.
I generally start with the "big" E string. (The one closest to my face). And lower it a little bit, I tune the guitar back up to my normal tuning, and if I like it where it's at I leave it there.
If I don't like it I can raise or lower it untill I do like it... just let off the tension, adjust, retune, play around, and repeat untill you get it right.
When you get the "big" e right, take the tension off of all the other stings and lower them to back the same level. Retune and see if you like the guitar where it's at now.
If you don't play around with the individual strings untill you get something you like, but try not to have any really signifigant jumps or drops (it won't feel right when you're playing).
Ok if you've got that done and really just want to go all out you can set your intonation, because you've done a good job with the string height, and you've already got your tools right there.
With your guitar is PERFECT tune (it doesn't matter what that tune is, if you usually play in drop C, then tune the guitar to drop C). And start with either the top or bottom string.........
What you're going to want to do is pretty simple. Play the string open and triple check it's tuning, then play the same string on the 12th fret. Is the note at the 12th fret is perfect tune with the string being played open?
If not you have to adjust the saddles fowards and backwards untill it is. I believe fowards makes the note a higher and backwards makes it a little lower. (It's been awhile since I've done any set up jobs).
Make sure everytime you move the saddle fowards or backwards you check the strings tuning OPEN again. Once the open tuning is right, then check the 12th fret, and just keep on adjusting.
You probally won't get it pin point perfect, (you could play this game all night trying to do that). But I bet you can get it noticable better.
Now you're saying "holy shit I can't believe I did all of this"..... well I teach you one more little snipet..... The height of your pickups makes a huge difference in your tone and it's not hard to adjust.
Raising them a little bit will give you a more trebly tone and lowering them will make your guitar sound more bassy. Just think of them as a giant tone knob... higher and lower....
And congratulations, you can now apply for a job as a guitar tech! I got a little tech-ing job repairing guitars for a pawnshop in high school. They would basically just call me up and ask me if I could come set up some really nice guitar they just got in, or say something like "wil the guitars humming really bad, you think you could take a look at it".
Anyways long story short, I got a full time job with them in my junior year in high school, because I had done a lot of tech work for them, for way cheaper than the "tech" down the road would do it.
Pretty cool huh? If you need anymore set up help just lemme know.
