We've got 600K+ pages indexed by Google and have submitted our same sitemap.xml's to Bing, but have only seen 100-200 pages get indexed by Bing.

Is this fairly typical?  Is there anything further we can do to increase indexation on Bing?

yeah, unfortunately we've checked all the items you listed and there's nothing obvious.  seems like blocking pages is the only option left..

We recently made some updates to our site, one of which involved launching a bunch of new pages. Shortly afterwards we saw a significant drop in organic traffic. Some of the new pages list similar content as previously existed on our site, but in different orders. So our question is, what's the best way to diagnose whether this was the cause of our ranking drop? My current thought is to block the new directories via robots.txt for a couple days and see if traffic improves. Is this a good approach? Any other suggestions?

Is there manual intervention required for a site that has been flagged for duplicate content to get back to its original rankings, once the duplicated content has been removed?

Background: Our site recently experienced a significant drop in traffic around the time that a chunk of content from other sites (ie. duplicate) went live.  While it was not an exact replica of the pages on other sites, there was quite a bit of overlap.  That content has since been removed, but our traffic hasn't improved.  What else can we do to improve our ranking?