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>(snip)does anyone know if you can append .pdf files together?
Yes. You can add pages and rearrange their order in Acrobat. You can
also develop a TOC that links to separate files for chapters.
You can have two versions of a TOC. You can create bookmarks and you can
make links out of an existing TOC in the paper form of the document.
Check into a plug-in for Acrobat called Compose. It is a pretty stable
tool and it will automate putting links in, and creating bookmarks, out
of large amounts of converted documents.