In a nutshell, we've moved all our sites over to a new platform this year (with a new template, on-page optimizations, etc.), but a few of them haven't seen much (if any) recovery from the change, and it's been 4-5 months already. One site in particular is having issues I'm not seeing anywhere else - when I look at our Moz reports, the majority of keywords that are ranking are only ranking the https version of the homepage (it looks like the https version wasn't picked up and ranked until the beginning of October. Interestingly, the beginning of October is also where WMT shows a huge drop in clicks and impressions. We're still working with our dev team to implement proper canonical tags for the https page, since some pages are secure, and others aren't).
I don't think we're seeing a technical issue, since no other sites are having this problem and they're all basically copied from the same template. I've crawled the site, etc., and nothing has come up from that, and I've done a site search and Google shows all the pages have been indexed. I've also done a year over year landing page/categories analysis, which shows that organic traffic to the homepage had increased a lot and categories (and products) completely dropped.
We're wondering if it might be a link authority problem. The only other pages that are ranking are a few gender neutral pages that also existed on the old site. The navigation was drastically changed from product types (Boots vs. Shoes) to being gender specific (Men's Boots, Women's Boots, etc.). Other sites that we've relaunched have new category pages that are ranking, but I don't think any other navigation changed as much as this one.
I've gone down a bunch of rabbit holes trying to figure this out and keep hitting dead ends. Does anyone have any thoughts as to what happened or what else I should look into?