Can you show us a screenshot on 4 pages with the numbering you want!
I don't think your intended plan will work...
Is your printer driven by a RIP? I expect it is if it can perform staple (and you mention mixed media). What RIP - Printer model?
Staple operation always happens at the end of a multi page document. To my knowledge, Fiery - Command Workstation, you cannot force a staple at a pre-defined length; it would be convenient if you could however.
If you could force a staple at a defined range, 2 sheets, simply set the copy count at 2, uncollated.
I'm thinking you could create the job without duplicating your pages as intended and export to PDF. From there I would explore a few options.
Do you have any imposition tools for Acrobat? Quite Imposing or PitStop?
I would use Quite Imposing to duplicate all pages as you posted. You will end up with (in your scenario) one 4000 page pdf.
Than use Acrobat's Split Document feature. Set Max Pages to two. Set a destination folder. You will end up with (in your scenario) 2000 two page pdf's.
Change the printer's Print Defaults or create a copy/clone with Staple, or create a hot folder with appropriate actions (staple). It depends on what you are familiar with.
Highlight the destination folder or multi select files. Send all to the printer or drag into CWS.
How much of the above are you comfortable with, need clarification, is not applicable?
Just my thoughts - in short, to my knowledge staple happens at the end of a job - you need two page file(s).
Create a 4 page file for testing.
There is a way to have a side by side page number. Let me tell you the way how i am doing on it. See the images
1. Open up your file. There is a master page applied.
2. Insert one blank page before the page no 1.
3. Now select all the pages and uncheck the "Allow Selected Spreads to Shuffle"
4. After that you will see a bracket around the page number. Select the page no 1 (inserted blank page) and delete it.
5. After deleted the inserted blank page, the pages will be in a pair.
6. Right click on page no 2 and choose Numbering & Section Options
7. In the dialog box "New Section" check the "Start Page Number at:" and type the page number and hit OK button
8. After that a warning dialog box might appear just read it and click OK and do it the remaining pages.
9. See the black head on the top of pages. It is the mark of section.
Hop it will helps you for the side-by-side page number.