Thanks so much for your response.
Honestly I'm still not sure why or what happened.
Essentially the domain has a bit of history. It's been up since 2008 and is very well known authority figure in the niche. The site was taken down by the Govt in their domain seizure crap and held for 13 months. They had to give it back because they had no probable cause, and we were innocent. It's been a big issue in the media, especially when all the SOPA madness was going on but not sure if that 13 month disruption caused any issues for us.
When we came back up we were doing really well, ranking very high and doing about 5k visitors a day from google. We had our highest google traffic day on March 4th and then for some reason we did a massive free fall. Google just left. When I searched site:dajaz1.com it showed paginated pages, category, tags, search pages ranking, it stopped ranking our post pages.
I started going through the site to try and figure out what was wrong. I set everything that's not the home page or the actual post as noindex, follow, we started working on writing more, better titles, better seo urls, removed the pagination plugins etc. We're often the originators of content and sourced as such so it's not necessarily an original content issue.
Google bot came back, but it's still not ranking us like it was and now ranking people above us who link to us, source us, or copy our content. When I check site:dajaz1.com now it's at least pulling posts, but it's pulling posts with numbers in the url, or very old urls. Our newer posts are not ranking. We were getting 5k-8k unique visitors a day organically, now we're getting less than 1000. I'm still at a loss as to why and how to correct.