All of the things listed above and more can be found in the O'Reilly book Classic Shell Scripting by Robbins & Beebe. It doesn't just cover shell scripting but also sed, awk, regexes, manual pages, processes etc.
I second this.
The OP's question can be summarized as "How I get into Unix[like]?"
As this thread shows: there are several points about it, and several ways.
It's boring, pointless, and above all impossible to first study everything of what's it all about in theory, and then start working with it. You better just start working with it. Pick the tasks you need to do with your machine(s) (first could be to realize a
backup-plan), learn how to realize them, realize them, and then rate what you learned into the categories of the "jigsaw puzzle 'Unix'" which gains you the meta-knowledge what makes Unix so powerful, way above solving single tasks.
Those categories may be named as:
1. Shell. You already figured that out. You need to get used to shell usage. Unix means using the shell. GUI is an optional extra to the shell, not vice versa. The shell is where the power lies. And where most of the work is done. At least the work on and with the system.
Which shell is secondary. But I recommend to focus on sh, not bash.
At least for the start on FreeBSD.
You may add or change to (an)other shell(s) anytime later - or not. You better learn the internals first, before getting lost in the shell's features. The (important) internals are the same. What differs are the features (and some other things; but don't get us lost in details.)
Command line using will become computer usage by muscle memory, which means keyboard, not mouse shoving. That can only be trained by using it over, and over again.
Plus: Dig a bit into the shell internals (ls, cp, mv, rm, cd, mkdir, ln, ...), some core basic unix tools (cat, grep, find, wc, cut, paste, head, tail, awk,...) and an editor, of course. When combined you'll be amazed what you all can do with those! (For years I don't have no filemanager installed anymore. Don't need one.)
Plus: Dig a bit into shell scripting. This is not just the more sophisticated glue to make single commands, filters, and programs work together, but it's first choice to automate individual tasks on your machine(s).
That's what a computer is all about: automation.
Learning computering means to learn how to automate. Using computers means to automate jobs.
Anything else is consumption.
2.
Unix Philosophy. Find also other texts about it. Try to understand the ideas behind it.
For example: Name and compare downsides and benefits of either having many small, combinable modules to one large monolithic "jack-of-all-trades", while considering at each: learning effort and work efficiency short- vs. long-term, flexibility, adaptability, conformability, suitability, universality, maintainability.
See every unix[like] comes by its very nature as a software development platform. It may be very basic, but it's there. It's not for to write steam's next bestseller, but to close the gap of what the other tools may lack.
"All a dwarf needs is an axe." [Terry Pratchett]
3. A hunch of C. This maybe is already advanced, and maybe not really unavoidable necessary, but sooner or later you will stumble over certain issues you better have at least an idea of the underlying programming of the system.
C is Unix. And as long as most parts are written in it: Unix is C.
You don't need to master C. You don't even have to program in it, especially not your daily production. Though some things I rather and quicker do with a small C-source than in a shell script, while for many other things using C was a madness. They better be done with a few lines in a shell-script (See:
Master Foo and the Ten Thousand Lines), or in another language. Finding out yourself, which tools there are, what is used best for what, and above all what suits
you best, is part of the adventure.
But IMO kind of a slightly advanced beginner's class knowledge of C, a bit more than just "hello world" is very valuable not only to better understand Unix, but when you deal with things not only at the very surface, but start to dig a bit into system's details, even into shallow waters.
But, as I said: C is not top priority. Shell and Unix Philosophy first.
The book
fraxamo mentioned is a very good recommendation to get anybody from zero into advanced Unix usage on a very solid base, because it contains all the real important things.
Additionally I like to recommend Kochan, Wood,
Shell Programming in Unix, Linux and OS X, Addison-Wesley
It can be used as a prelude to the first book. It does not cover that many topics, does not dive as deep into them, and does not bring you as advanced, but therefore it gets you quicker into the basics.
the single most important thing when learning *any* file editor 
