Re: intonation adjustments?
After getting your action set to the desired height and the truss rod adjusted to get the neck straight...If you hold down the low E at the first fret and the fret that meets the body, there's should be a tiny gap between the bottom of the string and the 7th fret that's just barely enough to slide a thin pick through.
To fine tune your intonation, you'll need only a tuner with a needle or a good rackmounted tuner. With the guitar tuned to the pitch it'll be played in, start moving up the neck from about the 10th fret to the 18th, making sure all those notes read dead center on your tuner. If any of those notes are flat, move the saddle toward the neck. If those notes read sharp, move the saddle away from the neck.
Anytime you adjust that saddle, make sure all the open notes are in perfect tune again. Do this on all 6 strings till every note on the fretboard reads dead center and your tuner's needle is straight up. It sometimes takes a few hours, but the end result will be a guitar that sounds perfect on all chords and stays in tune like a dream.
If you're using a Floyd, it's more of a pain, but you have to do the same thing.
On a Floyd, make sure your base plate is always level with the guitar's top as you're doing the intonation, so when you're done the base plate is level with the top, the guitar plays perfect, and all those notes read dead center. If you do that, you can dive bomb till your heart's content and the guitar still won't go outta tune.