I am hoping to get some help from all of the brilliant SEO minds that post here on a question that I have been struggling with for a while.
We have 3 eCommerce websites. Two of the websites are niche stores that do well and do not seem to be having SEO issues. The other website is the "parent" website that these stores spun off from years ago. The main website got hammered by the first Panda because we had the same items and section pages on the parent store and niche stores. We went through and rewrote most of the content and that didn't help much at all. About 4 months ago I Noindex/Nofollow'd all of the item pages on the parent website that were also listed on the niche stores but left the section pages. It seems that the main website is still being disliked by Google.
My question is what to do next. My plans were to go and Noindex/Nofollow the section pages that are on the niche stores. Ultimately, I think the best solution would be to canonical from the main site to the matching niche store page but I am really concerned about the niche stores getting hammered because of this. I certainly do not want to drag those websites down.
I would greatly appreciate any information or suggestions that you guys may have. Thanks so much in advance for your time.