I keep coming back to this article 2011: The Year Google & Bing Took Away From SEOs & Publishers in response to questions about why some metrics seem a little wonky, why we are having trouble monitoring our links, and why we can’t use Google result totals as measurements of keyword interest when Google Adwords does not have enough data. Luckily, there are some other options to look into as well as suggestions for possible workarounds.
I’ve started using Blekko for some of the same functions Google once provided and although Blekko is not perfect, it is certainly much more transparent with its data.
Here are a few links for guidance in getting started with. One hint, creating an account is free and gives you access to all sorts of data and tools.