Organization and Citation Guidance Needed - FOIL and CMOS.

I need some advice on how to best document and process documents that were received via a Freedom of Information Request. The FOIA request returned which contained thousands of comments/documents that were submitted to an agency; in two different formats.

Comments and documents which were submitted via the agency’s website were sent as a database file (each comment document record has a unique ID from the database, with each commentator also provided with a unique id # (although it appears that some individuals have multiple IDs).

While comments that were physically submitted via postal mail or physical delivery were scanned into PDFs which are based on which of the 77 storage boxes they are physically stored in (each box was done in multiple PDF batches) each PDF contains one or more document.

I am going to be quoting from individual comment records/documents as part of my project. What would be the best way to do this? Do I create a new Zotero record for each comment that I use? Or is there a better approach?

I will be using Chicago Manual of Style formatting.

Thanks in advance for your guidance and assistance.
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