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Books are outdated and lack of many basic tips if you are looking for link building knowledge. On the other hand books are very precious source if you want to learn on page SEO and white hat techniques. I would recommend: Search Engine Optimization (SEO) Secrets by Danny Dover
I use also SeoMoz toolbar for more accurate results and comparison. MozTrust for example is almost like real time page rank but unfortunately can't reflect Google Page Rank penalties.
Sometimes Google is deindexing duplicate content but sometimes sites are only experincing drops in rankings. The safest way is to place noindex tag on your duplicate content pages.
In my opinion You should subbmit your site to like 50 most popular Social Bookmarking sites jut for the sole purpose of links. You can promote them further for the traffic if you have the time and skills
My fried had similar issue. Was trying to reach ant Google representative but they told him to wait and he waited and waited....
Th whole situation was strange because his site was brand new and had almost no traffic