Although not taught in this manner, I learned all of my basic grammar from http://www.guidetojapanese.org/learn/grammar (Tae Kim's Guide to Japanese Grammar). I've seen a lot of text books, but for me this was by far the best. There is a famouse Japanese grammar book that's written in Japanese and starts out writing with simple grammar to kind of bootstrap you, but I can't remember what it's called.

However,most of the stuff like the above that I learned actually comes from an NHK programme, "Kotoba man". It went into the history of vocabulary and grammar and after I watched as many episodes as I could find, the structure of the language really started to make sense to me.

I think part of the problem is that most prescriptive grammars for language are subtly incorrect. For example, what part of language is blue in "I am blue"? What part of the language is it when in "Blue is my favorite colour"? If they are different parts of language, what is the difference in meaning between the two? What if you said, "I am painting"? Or if you said "Painting is my favourite hobby"? What is the difference in meaning between the 2 uses (if any)? Is there a difference in the meaning of "am" between "I am blue" and "I am painting"? I think if you follow the prescriptive grammar of English, it will force you to answer the questions in different ways than your intuitive (internal) ideas. Or at least it did for me. Studying that sort of sentence in English helped me to study similar sentences in Japanese and puzzle out similar insights (or at least as imagined by me). YMMV ;-)