I thought I should post how I resolved this problem. I paid for an upgrade to Adobe (DC), which allows one to combine multiple PDF files. I convert my Word (unpublished) chapters to a PDF, drag all the discrete pieces together in the order that I want them, and then combine into one document. This also allows me to remove the pages (or sections of pages) with references and add in a full reference section at the end of the document, as well as include natural pagination for the entire document.

Eek! I think it's too late for that clever solution but maybe it will help some other poor soul.

Thank you; those are very practical and helpful suggestions. I hadn't actually considered pulling the whole thing together as discrete PDF's which I think may work better all around, so I will experiment with that option first and go from there.

I am pulling my thesis together, with 4 published chapters. The university says published papers should be included within the document, maintaining the formatting as they have been published. I have figured out how to do this two ways:

1) Convert the PDF to a Word document. This is much cleaner to read, but the sizing can be tricky to format into an A4 and, more critically, I have found that with at least one of my papers it messes up the scientific notations (They are basically free-floating around in the paper rather than staying within the sentence structure.)

2) Save each page of the article as its own PDF and then insert it into the Word document as an object, page by page. This is easier in terms of spacing and pagination, however the quality of the formatting is poor - it looks very fuzzy. I am worried when I convert it back to a PDF as a full document it will be even harder to read.

I have looked at other theses and their inserted papers look very clean and crisp. Does anyone have practical tips on how to maintain the quality and the formatting at the same time?