Our Strat's frets have been replaced at some time and they're in pretty good shape, so all that's needed is a good polish. If the lacquer has worn on the fretboard, it sometimes helps to mask of all but the frets: if you don't, the dirt from the frets will go straight into the grain of the timber on the fretboard. A word of warning - use only masking tape, as a stronger tape can literally pull the lacquer away when you remove it. Even with real masking tape, I generally pre-stick it to the sheet on my bench first to make it less savage. Use metal polish to clean the frets; it's slightly abrasive and will make them look like new. One last thing: look at the headstock and check that the string-trees are nice and tight. If they're rocking around, the strings will not stay in tune.
Now it's time to replace the strings and tune up to pitch - make sure you don't have more than three turns of string around each tuning post. Too many wraps means it needs more tension on the string to tune it to pitch, making the guitar harder to play, and it also makes it harder to tune the string accurately.
Now's the time to set up the tremolo, the intonation and the action. Most people go wrong by having the tremolo tilted too high; they work best when the back of the tremolo is about 3mm - a matchstick's width - off the body. To pull the tremolo back, the springs on the back of the guitar must be tightened, and to let it forward they must be loosened. Adjust the playing action and the springs at the same time, because since the bridge is a lever, one effects the other. Make only small adjustments at a time, tuning to pitch after every operation.
When the action is right, set the intonation. Tune each string in turn to pitch, and fret it at the 12th fret. If it's sharper than the 12th fret harmonic the saddle needs to be moved backwards, and if it's flat it needs to move forwards. It's possible to check all of the notes on the fretboard and adjust with a bias towards playing in one key... but unfortunately it only works for one key. The fact is, it's impossible to make a fretted stringed instrument play perfectly all the way up and down the fretboard. If it's right at the 12th fret, it should be acceptable everywhere else.
Finally, replace the cover plate on the back. If the screw holes are worn you can fill them with matchsticks and wood glue, then cut off the tops when dry, and
re-drill. Check the tuning and the bridge again; if necessary, adjust the truss rod so that the neck is ever so slightly concave.
And that's it. You've just completed a Strat overhaul that should keep you playing in tune for plenty of time to come.