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php is great at generating pdfs, but i dont think that would help you here, because it would need smaller chunks of the original source to write from and if you have that, why not just display it in a more web friendly way.
going backwards from pdf is just messy anyway you try it. i'd concentrate on getting the articles in another form before they get pdf'd. unfortunately i dont have any personal experiance with indesign, but a few reviews say that indesign 2 supports output to html or xml, and indesign files are compatible with indesign 2.
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