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A clickable phone number is great for mobile landing pages. Try wrapping the number in a highlighted box and place at both the top and bottom of the page.

SeoMoz members have no control over what Mozbot crawls. Your best bet is to use a variety of site explorers to find links. Ex. Majestic, Google Webmaster tools, Link:www.example.com, Bing Link Explorer

Do you know the exact date you traffic went down. You could have been hit by Panda. There were two Panda updates before and after Penguin in April.

Try this analysis to get a better understanding if you were hit by Penguin or Panda:

http://www.searchenginejournal.com/penguin-or-panda-how-to-determine-which-google-algorithm-update-impacted-your-website/43751/

Have you created and submitted a XML sitemap to google through webmaster tools?

Also, Seomoz recommends limiting the links on any page to less than 100. The reason they state is "When search engine spiders crawl the Internet they are limited by technology resources and are only able to crawl a certain number of links per webpage...though if your pages have a high page authority, search engines will usually follow more links."

With this in mind I would consider building links to deeper pages on your site to help build authority and help google find some of these pages that aren't indexed.

Create custom landing pages that are relevant to your ad copy and set a budget. Make sure to do plenty of keyword research and utilize positive and negative keywords on each campaign so your ad is not showing up for irrelevant searches.

I agree with Kevin on measuring everything and using a unique phone number to track your leads.

I would work on building more quality links. It appears that a majority of your links are from directories and may not be helping build authority on search engines. Consider building links to your product pages with diversified anchor text to have a natural looking linkback profile. This should help get your product pages ranking.

Are all of the product descriptions unique other than the canonical issue?

I think Rankerizer - http://www.rankerizer.com/ - does a pretty good job of tracking your ranking for multiple keywords. And you can easily export results into a CSV file.