If you are able to use InDesign, there is an alternate method.
1. Create a single page InDesign file the same size as your PDF.
2. Go to Window> Utilities> Scripts> Samples> Applescript (or Javascript is you are using a PC)> PlaceMultipagePDF.applescript> Run (fly out menu, top right).
3. Now you have an InDesign file with a page for each page of your PDF. In InDesign add a page number to the master page, position and format it as desired. With the page number selected, go to Type> Insert Special Character> Markers> Current page number.
4. The page numbers will appear on all pages. In order to advance the page numbers, select page 3 and from the pages panel fly-out menu, go to Numbering & Section options> Start page numbering at 1.
5. Now all page numbers are correct, except page 1 & 2, to delete these page numbers, select these pages, overide the master page, then select and delete the page numbers.
6. Export to a new PDF.
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