"The book about the "Chandler" project (forgot it's title) is also a particular good read. Those two in particular are interesting reads about why things fail."
Dreaming in Code, by Scott Rosenberg. Highest recommendation. 10x coders hired by visionary engineer to scratch their own itch. What could go wrong?
Not "mystical" but "mythical" man month.
Go on to reading the Toyota management style in itself, there's a couple of books about it, that's what many IT techiques are getting their ideas from.
It's mostly about finding your values so to speak and pinpoint what you really think makes up a good software development company - maybe your focus will be on organization, maybe on other things, so get an overview first.
These two articles are hopefully also an interesting nudge to think about many things:
http://www.computerworld.com/s/article/9137708/Opinion_The_u...
http://alistair.cockburn.us/Characterizing+people+as+non-lin...
O'Reilly has a very interesting book with analysis which practices actually work and why/how - sadly I also forget the title. There's for example a chapter about when and why pair programming works and when and why not.
Also, just watch carefully and learn to notice "good organization" - happens in surprising corners and niches and try to see WHY it's good.