I purchased book 2 a long time ago, but I haven't used it and don't plan on using it. Heisig's first book was brilliant and I guess a systemized way to learn the readings for all 2042 characters is laudable, but I feel like after all that time learning the writing and meanings of the kanji, I'm better off learning stuff in context than doing a whole lot more memorization. Besides, just because Heisig conceived a great system for learning the meanings and writing, that doesn't mean that he demonstrated equal genius in book two. The learning methods in the two books are almost completely unrelated.
I guess if you were in a situation where you had to learn to read text without furigana in a very short period of time, you could do book 2 and then be in pretty good shape, but I've found that learning by reading young adult books with furigana, I'm able to pick up the readings pretty easily (usually furigana is only given the first time a word appears in a chapter), and I learn loads of vocabulary that way too.
One of the central methods of Book 2 is to group characters that have the same or similar reading and share elements (like 令, 冷,齢, 怜 all pronounced レイ). It's true that making note of such things is very helpful to learning, and if you can, you should stop and think for a minute when you notice something like that. Actually, one of the indexes to P.G. O'Neill's
Essential Kanji is organized with that idea in mind, with cross references to kanji that have similar writings but different readings.
Well that was a mouthful, but I hope it helps.