2.5mm from the top of the bridge pickup's pole pieces to the bottom of the low E (unfretted). That's the sweet spot for me, not just for my guitars but I find it's just about right for most of my customer's guitars too.
Obviously there are tweaks to be made depending on output - like some of the stupidly hot Dimarzios will be sunk a fair bit lower. But I find on average that any lower and you start to roll off the bite, and you don't get as much sustain and juice. You can get closer, but it's anybody's guess after that point. Depends on string guage, how hard you hit etc, but any closer than 2mm and you're definitely gonna run into problems. Hard to control, feedback, squeals, and weird treble artifacts. As well as your string being pulled out of tune and damping sustain due to magnet pull.
As for the neck pickup, I fret the last fret of the guitar and adjust it so it's the same distance away from the low E as the bridge pickup is. This results in an even balance across the fretboard, between both pickups. The neck pickup usually results in the bass side being dipped away from the strings a little further than the treble side to compensate for the increased bass in the neck pickup.