Start with this link. Read it, and understand it. Then apply it to your new bass.
http://www.fender.com/support/basses.php
Do you have the tools, and the knowledge to do this?
That link is a good start, but your bass can be fine tuned even better than that should you care to do so.
As far as final pickup heights go, that depends on a few different factors. What tone are you looking for? Do you want warm and round, low mids growly tone, top ended grind,..what? You can adjust your pickups to help in the final tone, so as to eq a bit less at the amp.