Joined: Mar 2011
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You can read Tae Kim's grammar guide (google), which is free.
Or you can read imabi's grammar guide, which is also free.
For a reference book(s), dictionaries of Japanese grammar are comprehensive and clear but expensive. I read the basic and intermediate edition from cover to cover while reviewing the sentences in Anki, and it has helped me substantially, especially the basic edition. But this method is not for everyone. It can be used to simply look up unknown grammar structures you come across.
Joined: Oct 2012
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Tae Kim might seem overwhelming at first. That's because it is. There's a simple solution for coping with overwhelming floods of information. Just let them overwhelm you. Then let them overwhelm you again and overwhelm you some more.
It's like standing under a waterfall, but only three quarters of its previous water amount will be dropped on you every day. It's like standing under it turns off the spring bit by bit.
And the analogy is like Shroedinger's Cat as a metaphor. On a physical level it makes absolutely no sense going from common logic, but when applied to the field it's meant to be applied to, it turns out to be correct, even if you can't fathom how.
Edit: Oh, and Mr. Scotch, I hope you had a nice hiatus!
Edited: 2013-02-17, 10:29 am
Joined: Feb 2013
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Thanks for all the great (and very quick) suggestions! But do people think learning grammar after RTK1 is the best step if my first - out of many - goals is to learn enough Japanese to read manga? The other major thing I have noticed is a large amount of words which I can only assume are pretty basic verbs in hiragana which for the most part I have no idea what they mean.
Joined: Sep 2012
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Not a fan, but Tae Kim will set you off with a good base. I definetly recommend bookmarking imabi.net and jgram.org for more explanations/examples; sometimes Tae Kim's explanations are brief so it's good to have other resources.