A few suggestions for possible reorganization. You don't have to have everything in one massive document. You can have a short summary, a longer report, and technical appendices in separate documents. You can have a paragraph or two on the Web site to motivate the reader, or maintain all the short summaries of all modules in one document with version numbers and a changelog. You can take all the meta-information (explaining what the purpose is of each section and subsection) out into a "Overview of Report Structure" document so it appears only in one place. You can cross-reference all these with clickable links in the PDF. I don't work with MS Word unless forced to do so, but I'm sure it can handle appendices without giving them chapter numbers. Just a few suggestions. This is obviously a labour of love for you, so do what you think is best for your readers.
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Got it.