The main problem issue is the fact you need to have DIFFERENT VBA modules in three different files. I am not sure why that is important, but if it really is, perhaps do this.

1 Verify current document
4 Save current document as original filename
2 Run VBA to remove modules & Saveas "FileName_Finalized_1"
3 Run VBA to remove modules & Saveas "FileName_Finalized_2"

This assumes the removal process is accumulative. If not then you may need to close and reopen original file. And of course you will need to come up with the VBA to edit the code modules.

Thanks for the response. Unfortunately, I cannot create document 2 from document 1 (or vice versa; they both require different changes to the content, and need to start from the original master). Currently, the changes to the VBA modules are the same for both, alhough I may also need to save each the documents specifically for version 2003- and 2010+ (doubling the # of documents I would need to create), which would require removing 2010 specific code modules.
This sounds like what I described in my last post (saving the 2 documents, then immediately resaving as the original master document), and I did a quick test which indicates that it should do what I want.