Those URLs do look like they could be used for the canonical links. It's not going to have anything to do with your DTD, however. The DTD is essentially directions to the browser's rendering engine and it doesn't have any affect on URL resolution.
As for PDF files, there is no way to place a canonical link in the html - because there is no html.
Last month Google announced canonical support in the http header [webmasterworld.com] and specifically mentioned PDF files.
However, that's not going to help with any copies of your PDF files that appear on other people's servers. I usually embed the original URL in the document itself, and also in its meta data.