Hey Jeff,
Just out of curiosity, why haven't you redirected one site to the other? Why have two sites in the first place? If these stores sell close to the same products, there is no sense in maintaining both of them. It just opens you up to issues like the ones you've described. You're literally competing with yourself for rankings on two different sites when you could most likely rank better with one site. Seeing as you've lost 75% of traffic, this seems like the perfect time to do that.
There are just so many benefits in terms of SEO and even resources. You're likely splitting your time in half trying to get each of these sites to rank which means all projects take twice as long as they should. Additionally, think of it in terms of domain authority/page authority. You have links split up to both sites right now, one might have more links for one category page than the other and that one might have more links to another category page than the other one. If you combine these sites and 301 redirect all the URLs from one site to the other, you'll combine the value of all of those links.
You can run yourself ragged trying to figure out what happened in a "broad core algorithm update" but the truth is, you'll never know. Your best bet is asking yourself what the risks are to having two sites to manage and, conversely, what are the benefits? Is it best to try and restore rankings to one site while neglecting the other or are you better off just combining your efforts?
In regards to the things you mentioned: Yes, the duplicate meta titles and descriptions could hurt you. They might make you look like you're scraping the other site which is something Google tries to penalize algorithmically. I would measure the results of those changes closely for the next couple months.
I'd also do a deep dive on page speed as Google made mobile page speed a ranking factor beginning on July 9th.
Hope this helps.
-Tyler