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The independent agency used a second site to build its rank - it was just a website with a bunch of big picture links to their website and a ton of textual links below. The website since then has been redeveloped and we implemented all of the 301 redirects, etc. to ensure no page rank would be lost, so there isn't any bad links from their website. The links in OpenSiteExplorer also seem to be legit. Still haven't figured out why they are ranking so poorly tho, it was put aside for now. All of the help has been greatly appreciated.

Awesome, makes way more sense now - Thanks a ton for all your help!!!

Awesome, thank you very much!!

Yeah it makes sense, thanks!!!!

That is exactly what we decided to do, the only thought (in my mind) is we'll working on two sites now (the switch will be approx Jan 2014) which seems a little redundant. Thanks a bunch for everyones input!