Good Question Luis,

Suggested Process below:

• Get a list of all your backlinks
• Make a list of all the known bad neighborhoods. You might have to research SEO blogs for this info
• Compare that with your list of backlinks
• You can also manually check any site to see if it is indexed in Google or not to confirm it's negative impact.

Here is a link to a useful post to get you started

Eric, try focusing on one location at a time in your title tag . At present you are trying to target 3 states ( MN, IA, WI) on the home page title tag. Build backlinks for the MN key phrase from quality sites. Be very careful with the over optimization penalty while you work with the on page factors.

Good question Carlo . If i had to handle that for the client, i would classify the links as "related content" or "related posts" which is a common practice with blogs and news oriented sites. The "incoming search queries" classification can be misleading and a direct suggestion that it is aimed at the search engine bots as opposed to the visitors.

You might also want to review this post below from SEOMOZ

http://www.seomoz.org/blog/how-to-train-a-link-builder