When I first started working with PDF, I found the PDF reference very hard to navigate.
It might help you to know that the overview of the file structure is found in syntax, and what Adobe call the document structure is the object structure and not the file structure. That is also found in Syntax. The description of operators is hidden away in Appendix A - very useful for understanding what is happening in content streams. If you ever have the pain of working with colour spaces you will find that hidden in Graphics! Hopefully these pointers will help you find things more quickly than I did.
If you are using windows, pdftron CosEdit allows you to browse the object structure to understand it. There is a free demo available that allows you to examine the file but not save it.
