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If you must, use xlsxwriter to write it directly into the Excel spreadsheet. This is kind of a pain. If you can get away with, say, writing the data to a CSV and then copy-pasting it into the Excel sheet, you should do that instead because it's so much more conceptually simple and works directly with the Python data structures that you parsed in Step 3. Automation doesn't have to be completely fire-and-forget to save you a ton of time!
I made a similar project where I matched sentences in a doc to sentences in multiple PDFs. Maybe it could help you. https://github.com/licjon/reference-finder