Introduction to Linux - Discuss most of the things that you asked like boot process, file system etc. and it's for the beginners.
Bash Guide for Beginners - Introduction to bash scripting.
Students Guide to Unix - Not a direct book of Linux, but great to begin any Unix system. This is the best book (IMO) for beginners who want to learn Unix systems like Linux. It discusses the basic things like what is a shell, how the man pages are organized etc. etc. And a full chapter on VI editor. The writing style of this book is also great. It's like reading a story book.
Beginning Linux Programming - As the name implies, it's the book to start programming on Linux. This book contains a chapter on bash scripting too. And also other development tools like gcc abd gdb, makefile, Linux process and threads, socket etc. It's a great book to start programming for Linux.
And there are numerous other tutorials, man pages etc. Just google for them.