Questions
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Large site with faceted navigation using rel=canonical, but Google still has issues
Yes that's a different situation. You're now talking about pagination, which quite rightly, canonicals to parent page is not to be used. For faceted/filtered navigation it seems like canonical usage is indeed the right way to go about it, given Peter's experience just mentioned above, and the article you linked to that says, "...(in part because Google only indexes the content on the canonical page, so any content from the rest of the pages in the series would be ignored)."
Search Engine Trends | | sichristie0