Questions
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Confused about canonicalization
Unfortunately, if your site is being indexed (and the duplicates are gone) but it isn't ranking at all, this may have nothing to do with the redirection. You could be looking at a more classic penalty, for various reasons. Have you run a header checker, like: http://tools.seobook.com/server-header-checker/ It's always good to make sure the redirects are doing what you think they're doing (they aren't multi-hop, 302s, etc.). Next step is to try very targeted searches - brand queries and long-tail queries in quotes. See if you can rank for anything - is it a total ban or just targeted? At this point, you've got to isolate the problem.
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