While researching why my
PDFCreator Add-in didn't work with custom page sizes, I discovered in the PDFCreator FAQs that like many printer drivers, it did not respond to custom page sizes and there was no override available in the driver. However this is fairly simple to work around by making 6"x9" a valid form size in Windows through Windows > Print Management > Servers > Forms > Manage Forms > Create a New Form.
This has the additional bonus that when you use Word's own relatively rudimentary PDF function, it too will adopt that size if applied to the document.