I know that sometimes a lens/body combo needs to be micro-adjusted to attain ideal focusing behavior, and that this is usually because of sample variation, but which parts of the lens and/or body are actually the primary causes of front/back focus?
It can be any number of different things. It all comes down to the tolerences that consumer cameras are built to.
Typical suspects would include:
It is all about the location of the focal plane as outlined here: What is back-focusing?