Fred,

> But I need to merge the separate PDF's into a single file; preferably with
> bookmarks for each file.

I use iText to merge a number of FOP generated PDF's together into one
single PDF.  I was also able to do page numbering across the resulting
single PDF which was handy.
 
This iText example code shows the basics:

http://itext.sourceforge.net/src/com/lowagie/tools/concat_pdf.java

I never worried about the bookmarks requirement so can't really comment on
that one.

Best regards,
 
Matthew Rea

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