HI Dan - thanks for looking into this.
Our traffic from organic search has indeed dropped (Google only, rankings and traffic from Bing/Yahoo have remained stable).
Hopefully we've taken care of all the shady back links via disavow. Like you said, however, it could be awhile before we know if this has had any effect. Most of the links you referenced, and most of the ones that needed to be eliminated, came from websites linking to content that existed on our domain prior to the agency purchasing it almost 10 years ago.
You're right about the unusually high amount of indexed pages. The inflation is from our blog "tag" pages. We've put a dofollow/noindex on all of these pages. They're pretty deep on the site though, I expect it will take awhile for them to be crawled again for de-indexing.
We actually had a 2-day recovery just over a week ago. Then, as quickly and inexplicably as the recovery came, we again lost rank on our generic terms. I'm going to add some of this info to the main post now. It certainly is bizarre, so I'm hoping someone might be able to identify what might have caused the site to recover and then drop again over the course of 48 hours.