You could use the re-director page approach that Sandy has documented on his blog here. Through the re-director page approach, you'd be able to see a person's subsequent web activities on your website even if they clicked the pdf file from a device that has no Munchkin association.
If you've added the links (external page/pdf) in your email as tracked ones, you'd see the Clicked Link activity for the clicks. However, you'd not be able to track activities/associate anonymous leads on the external web pages in Marketo, as Munchkin won't be present on the external pages. Also, by external pages, I mean the pages not owned by you, if you're trying to track the activities on the external pages owned by you (i.e., non-Marketo LPs), you could place the Munchkin JS on them to track the activities in Marketo.
