Quote From SEM:
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 I convert my Word (unpublished) chapters to a PDF, drag all the discrete pieces together in the order that I want them, and then combine into one document.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.