Right now, I'm using the Fender Setup Guide; however, if you look at Dan Erlewine's book, his basic setup is much different regarding relief (.012 at the 7th fret) and pickup height (6/64", treble side, and 8/64", bass side, for all pickups). And Bill Lawrence recommends a picku pheight of 1 nickel on the treble side and 2 nickels on the bass side.
With regard to pickup height, are you saying that you do the entire adjustment by ear, or do you preset the pickups as per Fender specs, then fine-tune by ear?
Yes I use Fender specs as a guideline and adjust from there to taste. Sometimes a particular guitar needs to stray from those specs, while others play fine to Fender specs. I think that's why Fender puts the (+/-) variations after each measurement called out. Changing string gauge will also change the specs.
I also have Dan Erlewine's books. The Guitar Repair Guide and the How To Make Your Guitar Play Great book. I don't know which one you have, but in the latter it lists the setup specs for many famous guitarists axes. And you can see that what works for one player doesn't work for another.
*It would feel weird for me to play Bill Kirchen's Tele with a huge amount of relief, but it works for him. If my Tele had that much relief, I would call it warped.
*Stevie Ray Vaughan, Eric Johnson, and Jeff Beck all play(ed) Strats, but they each have them setup WAY differently from each other.
It's all a matter of finding what is comfortable and sounds good to YOU. Good luck!