Don't know of any links/URL's, but ages ago, Guitar Buyer mag did a little supplement on setups, which was pretty good IMO.
Intonation: Tune the string to the harmonic at the 12th, then fret the 12th, still using your tuner. If there is no difference in the note on the tuner, then your intonation is spot on. If the fretted note is sharp, then you need to move the saddle BACK (towards the bridge) a bit, then try the note again, playing the harmonic anf fretted 12th. If the note id flat, then you need to move the saddle FORWARD towards the neck. Keep checking as you go, and only move the saddle say a quarter turn of the adjusting screw.
Tuning: Harmonic on the 12th.
Changing Pickups: The Seymour Duncan site has schematics that are quite good. BKP's have a small card inside the box showing the wiring layout.
Truss Rod: You hear loads of stuff about feeler guages etc, just don't forget that if you do adjust your truss rod, only do a little at a time, say a quarter turn again. Leave it to settle, tune up and play it a bit, if it still feels "wrong", then try again. Don't forget to let the neck settle after any adjustment, and don't adjust the truss rod too much at any one time.
Changing Strings: ? When they sound "dead". Check a guitar with new strings, and then try another that has an older set on. This totally depends on the individual, their preference of strings, etc, etc.
Frets: ?????
"Ebonizing" the Fretboard: Erm...Why? You could try rubbing some Lemon Oil into the board, that will make it a bit darker, or, get some ebony stain, and really, really carefully, paint your fretboard. Personally I wouldn't.
Generally, I do all my own setups these days, but, taking your guitar to the local guitar shop that has a repair service (especially if it has a good reputation) and getting them to service it and set it up for you is money well spent IMO.
Hope this helps (it may, however, be a load of old sh1t!). ;)