I'm pretty sure this is not automatable in Arbortext, eg. you would need
to embed the SWF "by hand" in Acrobat. However, I would love to hear if
what you want is possible to achieve with automated PDF generation
(direct to PDF or otherwise).
Just thinking, a clever workaround might be to roll your sleeves up and
write some clever Acrobat scripting that would find and replace certain
special images in your original PDF with the SWFs. You would need to be
pretty sharp with Acrobat scripting though I think.