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.