Partial match penalty & Penguin 2.1 smack

[CFSSEO]

Our site is large and allows business owners to post their inventory for sale.  We also make websites for those businesses that post their inventory.  We link back to the home page of our site from each of those business websites using our domain name as the anchor text.

Last summer we got a partial match penalty from Google

"Unnatural links to your site—impacts links

Google has detected a pattern of unnatural artificial, deceptive, or manipulative links pointing to pages on this site. Some links may be outside of the webmaster’s control, so for this incident we are taking targeted action on the unnatural links instead of on the site’s ranking as a whole. "

We investigated and noticed a large amount of links from spammy sites, forum signatures, blog comments, etc.  We think we were hit by a negative SEO campaign.  We started cleaning up the backlinks and disavowing them. Every reconsideration request since has been denied with more examples of these horrid links.

The final reconsideration request gave as examples of how we're violating Google link quality guidelines, our own sites we make for businesses.  "_Google has received a reconsideration request from a site owner for domainname.com.  We've reviewed the links to your site and we still believe that some of them are outside our quality guidelines." _

So here's the issue I need your advice on.  We have tens of thousands of business websites linking back to our main site using our domain name.  We're assuming this is the reason Google gave them as examples for violating link quality guidelines.  **How can we fix this without losing traffic from removing all those backlinks or make our traffic tank worse than it has?  **

1. Can we replace the domain name with our logo image and still link?
2. Can we nofollow all those links?
3. Can we link not to the home page but to internal pages or sections with no more than 10% of the links, linking to each section?
4. Should we just remove the links and cry?

[KarlBantleman]

Personally I'd no-follow them, you don't want them to pass on any ranking factors so no-follow the links if they are driving traffic. If they don't drive traffic then get rid of them.

Moosa is right though, you need to use other tools aside from WMT because that doesn't show a complete list of links to your website.

[CFSSEO]

We've been disavowing links found in G Webmaster Tools and Link Detox.  It took my resource 4.5 months to do 80k links.

Our business websites used our domain name to link to us.  As in 'powered by domainname.com'.  I can only assume that is why Google showed those examples in the latest denied reconsideration request.  Because we're linking from each site back to our site and they're all on the same C class IP.

Should we still link using our domain name, or remove those links?

[MoosaHemani]

Ok, I recently revoked the penalty after receiving three rejections from Google J. Here, I am going to share my experience with you and how I get over from the penalty!

-          The links that are displayed in the Google Webmaster tools are not enough, you have to search for more data from Majestic SEO, Ahrefs, Moz and more.

-          You can use Link Detox or Link Risk to see what links are risky for your website.

Try to remove as many links as possible and disavow rest of them.

As far as the anchor text are concern… always keep in mind that if you have lot of good websites that are linking back to you with a keyword in the anchor text, in that case you should use a strategy to diversify the anchor text or turn it in to the brand name.

In my opinion your % of brand name in the anchor text should be greater than the % of any other keyword in the anchor text (sign of a naturally looking website).

Plus at the same time plan a kick as content marketing plan that gives you natural links because this hints Google that now you are running at the right path!

Hope this helps!