Good reading

I picked up both of Greg Banish's books from Amazon.com.  I am about half way through reading Engine Management: Advanced Tuning and it has been great.  So far, we have covered a lot of the "why".  How engines work.  What all of the relevant terms mean.  The fact that, at its core, the PCM simply tries to guesstimate what mass of air is entering the engine so that it can add the appropriate amount of fuel to hit a commanded AFR.  So much "mystery" vanishes when you look at the core function of a product....inputs and outputs.

I am also spending a lot of time reading:
HPTuners forum
EFI Live forum (I do not own the product, but the theory is identical, so its good reading)

I have also read through Marcin's blog which covers some great topics from a mathematical modelling perspective trying to figure out exactly how something works.