You probably won't find a book containing everything that you want. Python is the language that the Foundation supports, so most if not all books are going be about Python. There is the Raspberry Pi user manual, written by Eben Upton. I've never read it, but I've seen it at my local B&N. Looks good.
As for C++, there's this great list which lists very good C++ books:
http://stackoverflow.com/questions/3882 ... e-and-list
I'm currently going through the Programming: Principles and Practice using C++, very good book. C++ Primer was a little too dull for me.
I would also look at a Linux command line book. I've never used one (just picked up the skills along the way), but it's a good way to learn Linux systems in general of you haven't used one.
You could also learn some Bare Metal, and guides exist online for this.
There are 10 types of people: those who understand binary and those who don't.