On the issue of pickup height, here is what I have found with my Jazz Bass, and other basses.
Raising the pickups closer to strings = more bass
Lowering pickups away from strings = more treble
My jazz was sounding unpleasantly thin. I raised the pickups substantially (actually to the max I Could go without hitting the strings while playing. This gave me the fattest freaking bass ever. Random people would comment on the crazy lowness of that bass. But that was to much. Lowering the pickups a little bit at a time, I found a point where there was more grouwl and definition. Also, lowering the pickups just a little bit yeilded a substantial increase in sustain. But it really is just setting it by ear.
When I set my pickup height, I set my amp at some moderate tones. Tones that are not heavy in any section of frequencies, but tones that are still good tones. While moving the pickups, I sample different positions on the guitar's tone pot as well (Most frequently between the 100% on and the 65% on positions.) Then I look for what is needed from the pickups. After adjusting the pickups, then I adjust my amp.
That explanation is awfully vauge, but it's trial and error mixed with some good understanding of what changes your making and understanding of why your bass sounds the way it does, and how you'd like it sound.