In your original post you also said that you pruned some dead wood, that would have also created a lot of 404s crawl errors, please check your Google Webmaster tools for these errors. Not to mention all the tags that you delete will also create 404s. You must set proper redirection for them too.
And… sometimes it is just better to start fresh with new website, because Google may or may not restore your website to previous levels regardless of all improvements that you will do and it’s the brutal truth.