Pup height is probably the least critical adjustment in the setup procedure. Because the height will vary from instrument to instrument due to varying pup magnet strength, there is no single "right" measurement that fits all.
Setting the pups too close can cause some wierd effects because the pup magnets will "choke" the strings, affecting thier vibration. Sort of like magnetic braking.
I usually start out about 3/16" from pup to string. If you pop and slap, make sure that the string doesn't strike the pup.
Hope this answers your question.
Harrell S.