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Without you providing additional information, basically you need to start working through your list and addressing the issues, based on which are the most pressing. You probably want to take a look at the Moz SEO guide and make sure you're following best practices in optimising the site overall.

I asked a similar question a little while ago, there were some suggestions there including: AnalyticsSeo and SEOanalytics, I haven't used either of those, but maybe check them out.

You might want to wait and see how the new Moz analytics performs, how the reports look. I understand Raven Tools are also working on something new atm: raventools.com/simple/

I'm quite eager to get my hands on both!

301 the additional domains to the one you want to focus on - except the domain that has the penalty, if you're certain it does.

Just noticed that Google Webmaster Tools is reporting Google Analytics virtual page views as 404s.

Shouldn't Google's own crawler be configured to recognize and discount URLs in Google Analytics code used to track virtual page views?

Wondering if this is just a short term issue waiting to be addressed by Googs.

One hour of downtime is not going to cause you losing all of your rankings.

I would advise having a look at the date you lost the rankings (is this tied to a drop in traffic in Google Analytics? You can get a date that way) and seeing whether it correlates to a date of a Google algorithm update.

On my very brief inspections, your links look like mostly directory junk:

http://www.opensiteexplorer.org/domains?site=4sharesite.com

So it's possible you may have been penalized by Penguin, but you need to inspect that further.