Your pickup height depends on what you want out of them. The closer they are the more treble you will have. Fender says 4/64 on the treble side and 5/64 on the bass side. Holding the string down on the last fret and measuring the distance. Thats for a standard strat. Humbuckers that are wired in parallel need to be a little closer. 3/64 trebel side to 4/64 base side. Custom pickups are another ballgame some hot ones need to be down low or they just over power the sound. Pickups also have a magnetic effect on the strings and will pull on them if to close. This is the standard answer, now what I do is.
I turn them down flush with the pickguard , set my volume on the guitar to about 6 or 8. Crank my amp up to where I like it, which is where the windows in my house can hear the sound, and then start to bring them up toward the strings. I raise them till I start to hear that trebley twang, then I lower them down till it goes away. On my Strat that has a humbucker and two single pickups there sort of stair steped down, humbucker high, middle pickup a little lower, neck pickup a little lower, I like that warm sound that i get.
Now my start that has 3 singles there all about the same height, maybe the neck pickup is a little higher for rythem.
My Telecaster is a whole different story we want the twang so it's set up to factory specs. I just haven't fooled around with it much to see what it will do. I like the sound it makes.
My Epi Dot studio Es 335 semi hollow body is a mystery. I can't tell much buy raising or lowering them. It sound great all the time, 2 humbuckers, independent volume and tone, it's a blues machine.
I have a frankinstrat that I do all my mods to, Seymore Duncans pearly gates Switching, up and down volume and tone knobs, There must be 50 combinations of tones, and believe it or not the pickup height is set about the same as a standard strat. Its all in how you hear the tones.
I've come to the conclusion that I can effect the sound more with the amp settings. I have a number of amps and they all sound different. This is just my opinon and I'm sure you will get a bunch more suggestions. I hope this helped...Jake :)