The official PDF Reference is very readable, see maest's link. Just start at the bit about the file structure and data types, then the basics about the commands in the Contents stream, the graphics and text states, then whatever takes your fancy. Later versions added some extra complications such as compression of the xref table and object streams, you don't need them unless you encounter them. Don't delve too deep into the bit about fonts unless you have to, it might bend your brain. A tool like qpdf to deconstruct a PDF to an uncompressed form is very handy.
> A tool like qpdf to deconstruct a PDF to an uncompressed form is very handy.
Forgot to say this in my reply, likewise pdftk's uncompress option is my #1 stop for learning about how a PDF is built when we have issues. You can poke around and hex edit for learning too.
It is easy in an uncompressed PDF to comment out a line with % to remove objects that I think are causing issues without messing up the xref offsets. Using a fully fledged tool to edit may have side effects in how things are rewritten which ruins the point of the investigation.
Acrobat Pro has some very useful features too, but not everyone has access to that.
The spec is really well written, and will take you far if you just want the basics (i.e. not the scripting stuff they added after 1.4 which is around where you should usually stop if you just care about printing). My only issue with it is when it comes to fonts or images, you'll have to break out to additional specs to understand those formats since PDF is more of a container.
I do like this minimal example as a way to get started and see how a very basic PDF is built.
