I'm busy updating this series of articles for Muse mag:
http://ratcliffe.co.za/articles/setup.shtml
I'm up to nut action with the rewrites, but pickup height is a relatively new article anyway. They are pretty condensed now thanks to a 800 word limit for an article in the small format of Muse, but the pertinent info is all there. When I get a chance, I'll try slip in more pics for a more illustrated guide.
For electric, I can also highly recommend the book
How To Make Your Electric Guitar Play Great! by Dan Erlewine.
EDIT: Good points Bob - as mentioned in my truss article, I've seen a lot of truss rod "action adjustment" ...some of it fatal. Generally if you do things in order though, you won't have any problem, but doing something like cutting the nut and
then only lowering the bridge is a recipe for disaster.