"How the sausage is made" tour of apache/php/mysql interaction
PHP and MySQL by example has a pretty basic picture of the process, which I think you probably already understand.
Getting more in-depth than that picture though is a pretty long discussion. Ironically, you can read the book I just linked for a pretty good description. If you have more specific questions, I recommend opening new questions for them. Enjoy!
I have found a site that has, at least in part, contents from the book Advanced PHP Programming by George Schlossnagle.
The site is located at: http://php.find-info.ru/php/016/toc.html. Specifically, the section on The PHP Request Life Cycle contains a lot of the nitty-gritty details, including some source code and diagrams.
DISCLAIMER: IANAL, but considering that the book is still listed on Amazon, its possible the content linked to above breaks all sorts of codes, rules and/or laws. Its not my intention to proliferate or condone illegal or pirated materials, so if that be the case, please remove said links.
You are correct in the fact that there are entire books written on how this all fits togeather here is a link to a "walkthrough" it touches on the main parts.
http://computer.howstuffworks.com/web-server.htm
Hope it helps