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Wow. "Yes, there is some lose of "link juice" through a 301 redirect. I can't give you a precise number, but most SEOs believe it's about 80%." I had no idea it was that much. I have also never heard of having two sitemaps, for old and new urls. Glad I ran one BEFORE making massic 301 changes to site structure today! Will throw the new one to Google but keep the old one. Thanks for the tip!

If you have duplicate content across multiple web presences on the same server, then yes, you may have a problem.  It's likely best to go to some effort to differentiate your content and make sure each site is unique.