I highly recommend this book: http://www.amazon.com/Japanese-Step-Innovative-Approach-Spea... as another excellent resource. Written by an engineer for engineers, with detailed flow charts for the various conjugation rules and other aspects of the grammar.
The book lists the various common sentence structures then teaches you how to expand the various fragments to construct more complex sentences. Somewhat similar to learning via a CFG and deriving a parse tree. if you want to absolutely nail your Japanese grammar, this is a solid logical way to go about it.
Book's biggest drawback is that it is rather dry. You will need to complement it with a book that focuses on vocabulary, idioms, and colloquialisms so that you don't sound like a robot.
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