First, "do/done the documents' is not a standard phrase. People 'write' or 'create' documents. I can imagine someone saying 'make the document,' but it would be odd. If the person did not write or create the documents, I am guessing that might mean that the person only made copies of the documents.
Second, your two alternatives ('you made for me' and 'I had done') say two different things about the documents, so they can't be switched without changing the meaning. Who made or created the documents--the speaker or the person who is spoken to?
Okay, I understand now. Adding 'by them' after 'I had done" makes it clear to me.
This is clearer and better: This is to request a copy of some documents you made for me in November 2000.
This is grammatically correct: This is to request a copy of some documents I had done in November 2000.
...but it would need to be spoken or written in a context where they KNOW that they were the ones who created the documents.
I'm also wondering about 'some documents,' 'the documents,' and just plain 'documents.'
Use 'some documents' or 'documents' if they created several different documents for you in November, and the next sentence tells them the precise ones that you want copied now.
Use 'the documents' if you want copies of all the documents they created for you in November.