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Here is a easy way to do link profiling from Dr. Pete:

http://www.seomoz.org/blog/link-profiling-with-open-site-explorer

If you are a pro member you can see all the link data.

Once you identified where your site is lacking when it comes to links from similar DA as your competitors, once should start with the areas where your site needs most work.

Hi sorry I have read your initial question more in detail and did some further pondering and research and as I understand it, according to Google's places quality guidelines if you are moving all the store locations to best ranking domain as sub folders you should still only have one listing for the central store and add service areas.

You can go that way but then you will loose two possbile places listings. But then again on the other hand some one can report the listings as is to Google and they can remove the listing and see it as duplicate listing.

http://support.google.com/places/bin/answer.py?hl=en&answer=107528

I would do what you suggested above accept only keep one listing as is to best ranking domain and then edit the listing with service areas if not already listed.

Even though they do not say this in detail in their help I am sure Google might flag your edit if you point to an existing domain places listing.

Hope this helps,

I would also start by identifying the sites that brought the most traffic or money, I presume you running Adsense on these sites (side note also remember to have less ads above the fold since last layout update from Google).

The sites that are performing the best would be the ones I start with first when it comes to redesigning and making sure there is no further inter linking to the other sites.

Also make sure they are different CLASS C IP's.

After panda there has been a few people that would create sub domains saying that this worked as lets say all content that is related to yellow went to yellow.domain.com and red to red.domain.com.

Why I am bringing this up I think you should maybe look at this and be sure if moving to main domain as sub domain that Google Panda will not penalise the over all site, this can be prevented by making sure you not moving over any of the old content that was low performing, if there is some of the old content that was low performing I would improved it and the move it over to sub domain and 301 redirect as you said to the new sub domain and content that is better when it comes to post panda on site seo factors (if this makes sense).

Here is a interesting forum thread you could read that might influence your decission.

http://www.webmasterworld.com/google/4394776.htm

Hope this helps,