Literacy in Japanese is more difficult than some other languages mainly because of kanji. The large number of kanji to learn makes it seem impossible at first. Also, it can be hard to memorize the kanji because, while the shapes are relatively simple, by the time you learn 500 or so you start forgetting the early ones-- unless you establish a regular system of review.
In my four years of study of the language, the best review system I have found is Mnemosyne. And it's free!
As for actually learning the kanji, the Kanji in Context books are hard to beat.
And of course you want to make sure you have a good dictionary.