Hi Rand,
Thanks for your reply hope you've enjoyed the holidays. A hidden manual penalty could be it may be applied to main.com as it doesn't even rank for a direct name search as far as I'm aware there is no 'bad' seo on this main.com domain except for the dupes which were an accident.
There are only ~50 incoming links to main.com but that was enough to rank for some target keywords. The sister site may have had some bought backlinks though that was before my time but that still ranks for a direct name search. That brings another question is it worth cleaning these up? I've been slowly compiling a list of the links that are bought but at the moment am not disavowing them as I don't think they are currently causing a problem.
Looking through the numbers our rankings have been on a decline since May and we will have to continue the SEO battle. Though in the mean time we are looking at solutions to bring in some cash flow such as adwords and letter drops to local businesses.
The suggested CPC is quite high would you suggest bidding at a higher or lower price? They are quite low volume keyword searches but are directly targeting our profitable market. The high volume keywords while relevant to our site do not directly target our profitable market so we are avoiding wasting money on these keywords as the CPC is the same.
We are also working on new content for the adword campaign to increase the conversion rate of these viewers.
Your blogs and tools have been very helpful for us,
Thank you