Trouble ranking
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I have a site that got messed over pretty hard by a BigCommerce issue. They used to rank but then Big Commerce had a glitch that set every page on the site to a https which was auto set, by their system, to not be indexed. This caused the entire site to go missing. It was then fixed by me, only to have the same glitch happen again. I again fixed it, and BigCommerce released a patch to resolve the issue. They admitted blame to my client and said it can take a while to resolve.
It has been a few months now, and google is slowly recrawling the site. It has about half the pages indexed. The pages that are indexed do not rank at all. I was wondering if you guys see any major flags that would cause this or if it is still related to the big commerce glitch.
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I see a lot of junk in the link profile, such as:
- proinfolink.info
- topseodirectory.co.uk
- netdirectoryltd.info
- seosong.com
- seolinkdirectory.co.uk
- netsitedirectory.info
- ilinkindex.info
- dsubmit.com
- seorganix.com
- seolistworld.info
- bestsubmitsystem.info
- etc
You might consider cleaning those up and focusing on earning some awesome links

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Noah,
Did you ever received any unnatural links warning or a penalty from Google ? Are you verified in Google Webmaster Console ? I agree with David, try to clean up those directory links and see if you can build some real links like a real business would have. There are some great articles here at http://moz.com/blog/category/link-building if you need some ideas.
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We have not gotten any warnings from webmaster tools. All of these links were on the site before we started. And the number of poor links like that are fairly minimal. They do not have a ton of links to begin with and I do not imagine directory links, which were valid in the past, would harm them like this.
The links are not in the form of blogroll, paid links, irrelevant sites, link lists, or anything like that.
We have been building them links through guest blogging and local university discount programs.