This is a brief addendum to the post below from Nov-12.
Since then, I have acquired Microsoft Office 2013. Except for using Outlook 2013 (which I like a lot) I really haven't done too much experimenting with 2013. One thing I have discovered is: Word 2013 can convert PDFs to Word .docx format, and it does a really good job, most of the time. By the way, if your workplace buys certain Enterprise Licenses from Microsoft, you can participate in the Microsoft Home Use Program. This cost an unbelievable $10 and gives you a legal license for MS Office Pro as long as you work there and they continue in the Enterprise License program. Check with the computer folks at work.
One really nice benefit of using Word 2013 to convert PDFs is that in many cases Word can convert the PDF active linked footnotes/endnotes to Word's active footnotes/endnotes. When this .docx file is compiled in the Logos Personal Book compiler, the resulting personal book will also have footnotes that popup the note when the superscript number in the text is mouse-overed. This is tremendous, since that is one of the big problems with many personal books: most of us just don't have time to manually convert footnotes prior to compiling in Logos, and as a result, many personal books don't have functional footnotes.
I have experimented with converting some PDFs. I converted a couple of commentaries in PDF form from CCEL.org, and the footnotes are retained perfectly (as far as I could tell by spot-checking). I converted a couple of issues of the journal Themelios (available in PDF form from The Gospel Coalition). In this case the footnotes also came through fine. One thing I did notice is that some compound graphics, that is, graphics that were in the original source (from which the PDF was made) in the form of several graphics "grouped" together to form a single picture, don't compile at all in Logos. Another annoyance with some PDFs is that when they're converted, you can wind up with a bunch of words, phrases, and sentences that were in the PDF as all-caps, but convert all mixed between upper and lower case. (Looks like those poison-pen letters from crime movies.) This happened with Themelios. Conclusion: if you want a Themelios issue, pony up the $2 and buy it from Logos. [Edit 7/17/2016]: For the last couple of years, Logos and The Gospel Coalition provide the Logos edition of Themelios free when each issue is published.
A couple of caveats. One, the footnotes have to be linked, active footnotes in the PDF, or Word won't have any magical powers to make them active. It is possible that there are active footnotes that Word won't convert, but so far that hasn't been my experience. Two, a really large PDF might not even open. Word will report some vague error about not being able to open the file and stop. In this case, if you really need the document, you could probably split the PDF up into two or more files and make it work. There are a number of free PDF splitter programs; search for "PDF SAM (split and merge)".
One more issue: you might get a notice from Word that certain interactive features of the PDF won't be imported. I have run into this when converting PDFs from CCEL.org; I can't tell that anything is missing. I think the notice is referring to the links to the resident CCEL online Bibles.
To actually do a conversion, right-click on a PDF file in File Explorer (or Windows Explorer) and choose Open With, then Microsoft Word (assuming you have installed 2013). It takes longer to open than a regular Word .docx. When it has opened, simply save the file as a .docx.