Use the request as an index, with each question matched to the proposed answer and supporting records. Follow the stated submission instructions.
Preserve a clear filed record
Have counsel review any uncertainty, inconsistency or missing evidence before submission. Keep the final version distinct from drafts and retain the confirmation that it was sent. This method is an organisational aid; it does not replace current agency requirements or determine which documents satisfy a substantive legal issue.
Decide before drafting which questions you can answer completely and which you cannot, because the second group determines whether advice is needed. Use the request itself as the index, matching each question to the proposed answer and the supporting records, and follow the stated submission instructions exactly rather than a remembered process. Where an answer is partial, say so and explain what is being done about it instead of leaving the gap to be inferred.
Note against each entry who supplied the record and on what date, so a later reader can tell a document obtained for this response from one carried over from the earlier submission. Where the instructions specify a format, a cover sheet or a delivery address, follow the version of the instructions attached to this request rather than an earlier one, and record which version was read. Keep the index itself with the filed copy so the response can be reconstructed later.