If your use of Excel or the spreadsheet that you create requires complying with 21 CFR Part 11 requirements (as defined by your documented formal Company policies, SOPs, and risk assessments) then you must do so. Does this spreadsheet fall under a ‘medium risk’ or ‘high risk’ classification or is used in support of a ‘Quality’ based decision (directly or indirectly)? Your situation sounds like it does.
I think the answer to your questions is to manually log your incoming documents and track them on paper this will definitely make these controls compliant as it will not trigger 21 CFR Part 11! Then follow the qualification/validation process i.e. DQ(URS )/IQ/OQ/PQ and source a modern technology solution e.g. Data base that can be compliant to 21 CFR Part 11 and track your incoming documents with it.
As said by others avoid Excel as the pitfalls are well known and documented and compliance with 21 CFR Part 11is onerous if not technologically impossible without third party add-ons. Assuming that the documents you mentioned have been deemed cGxP critical.