Hey there, Phillip:
Good to hear you are cleaning house. I don't think it will be long before your rankings return. You have a good looking site, and getting everything "consolidated" in Merchant 5.5. is the way to go.
The /pet-odor/ directory you pointed out probably dates back 6 years and hasn't been linked anywhere in site in at least 3-4 years.
I just looked at the file the other day and said to myself, "Surely google knows that this page has been permanently moved after 7 years." So I took the redirects out of the htaccess file.
Three days later I check webmaster tools and google says it couldn't find that page. Checked my server logs and yes, googlebot had tried calling that page.
One other thing to keep in mind is that there is an SEO triangle, with the three points being:
Content, Structure, and Links
You already have good content (you mentioned that you have articles on your site).
You are working on the structure. Make sure your content articles link properly to your product and category pages.
Think about guest blogging or writing articles for getting links back to your site.
Ultimately, SEO is a passive form of marketing (even though it takes a lot of time), and you can never truly control how you will rank. So you also have to look at active marketing.
Hope this helps.
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