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so since you're doing what are all the right things generally, then I'd recommend looking at what the inbound link quality/volume/diversity is for various sites you have compared to their individual market competitors.  Beyond that it would need to be a case by case evaluation to better nail down issues/problems. On a final note, social's become a big signal and should be highly encouraged as well... (twitter engagement for example), though I know it's a challenge in that type of market.