Unfortunately the last few updates to the FeedWordPress plugin have not fixed the issues that I have been having. What is going on is that the meta data is not being pulled in to the individual posts when automatically searching for feeds and therefore it is not linking back to the original post.
I have setup a test site with a fresh install of WordPress and the FeedWordPress plugin that is updating correctly so it looks like I may have to kill my main site and start from scratch. The good thing is that I will be able to keep all 300+ posts that the main site has by exporting and reimporting via the WordPress import/export mechanism. My plan is to export the content, delete all the WordPress files including themes and plugins, and delete the db. From there I will do a reinstall of everything with fresh files and cross my fingers that it will work. It seems extreme but it seems the only fix available.
Wish me luck!