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Here is some additional great info on optimizing PDFs:

http://moz.com/ugc/how-to-optimize-pdf-documents-for-search

This article from Google Webmasters Central should solve it for you, Supporting Rel Canonical HTTP Headers

Mike

Hi Carl,

For the pagination issue, depending on the page content, you can either leave it "as is" or you can use one of the 3 methods referenced on SearchEngineLand.com for managing pagination.

And if it is a lot of different filtering and search results pages, you could choose to noindex,nofollow them (unless you want these types of pages to show up in Google's SERP) which would resolve your crawl issues with Moz.

You are correct in stating that these probably won't have a massive impact on rankings. For these types of issues, it more or less comes down to how tight you want to run your ship.

Hope this helps.

Mike