Re: Intonation
Here's a quick runthrough.
Put on new strings in the gauge you're going to use, stretch them out and tune them where you intend to keep it. Different tunings or gauges will scramble your intonation.
Using the saddle height allen bolts, adjust your action so the strings follow the natural radius of the neck, or how you prefer your guitar to play. Adjust the trussrod so that when the first fret and 14th are fretted, there's JUST enough space to slide a thin pick in between the string and the 7th fret (low E). Basically straight with just a little relief. Once the guitar is playing exactly how you like it, with the exact amount of curvature to the neck.....Time to intonate.
Tune all 6 strings.
Fret the 12th fret low E and see if it reads flat, natural, or sharp.
If it's sharp, move the saddle away from the neck. If flat, move it toward the neck.
Retune all 6 strings and move to the A, then D,G,B,E
After all the notes are dead center on the tuner between the open and 12th fretted,
move to the intonation 'fine tuning'.
Tune all 6 strings, then do the same intonation inspection on ALL the fretted notes from about the 10th fret up to the 20th. Try your hardest to get all those notes to read dead center on your tuner. Anytime you make an adjustment with your screwdriver, retune that string. By the time you're done, all the open notes and the majority of the notes above the 12th fret should be dead on.
After this intonation job, if any of the notes around the 1st or 2nd fret are bending sharp when fretting open chords, it's possible that your nut is not cut low enough.
This is a nagging headache to ANY guitar player. Unless you have proper files, it's best to pay a tech around $20 to reslot your nut. If you use any gauge above 10 on a stock guitar, this is mandatory, since fatter strings don't sit in the slot without binding. Essentially, your strings should be about a millimeter above the 1st fret.
On Floyds, intonation is trickier. First, you're dealing with the saddles being held by allen bolts, instead of the easier strat style bridge. You've got to get the Floyd baseplate flush with the body, so that at normal tuning it doesn't tilt forward.
Do that by tightening the 2 spring claw bolts on the back of the guitar.
When the trussrod and action are adjusted the way you like it, follow the same intonation rules above, only you'll have to loosen the saddle bolts and nudge them a little at a time till they're set right.
Keep in mind, if you change string gauge or use alternate tunings, including dropped D, your intonation will be off during that time. If you return to your normal string gauge or tune back to normal, your intonation will be fine again. Once the guitar has been intonated, LEAVE THE HEIGHT AND TRUSS ROD ALONE. If you move ANY bolt, allenbolt, or screw on the bridge, you'll have to recheck your intonation again.