A batch sequence in Acrobat can be used to do this. However, you will need to set up the opening preferences in Acrobat. In AA9, these settings are part of the Create PDF from Web. I think these settings remain for successive creations and so once you have the set, you could create a batch process for the large number of files. There are options for headers/footers, underline links, convert images, retain background, etc. You can also set landscape or portrait, margins, and such.
