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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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Placing the keyword in certain spots within your code will have very little if any weight into a site's ranking. You should provide us with the links to give a better answer as to why they may rank higher

For a generic page you should do keyword research and make your content focus around that. But write it naturally and do not stuff the keywords in there just because you can.

For your articles. make the title tag the name of your article. That is after all the title of the document. Those top ten lists and fun articles are great things to send out and do some link building with. If done properly you can obtain some good social awareness and links.

Using a local number on the places profile will help improve its local rankings.

You should have as many as you need. Do not create categories if there are no articles you can place within them. But do not group unrelated articles under the same category. Check into some keyword research to see if your broader categories get search volume and go from there.

For the example you gave, I would say to keep them all under a "branding" category and expand into those other keywords through articles.

If you have a more broad category it may get linked to more since it has more articles people may want. Therefore increasing its PA and ranks