Yes you are right. we put those internal pages in noindex to get better indexing for other pages and it really worked. But now gettting out of this penalty is our urget priority.
Conor, anchor text in backlinks has so much variety that it took 10 months to get ranking even for even secondary keywords. I was so afraid of keyword repeatition.
Site was not getting even 100 visits a day. I just want to get rid of many backlinks and changes just to rollback any changes google found on our site.