Managing large amounts of text/type

i’m building a site for a pharmacutical company. it’s a resource guide. it’s essentially a 300 page document, and turning it into a flash site, with links to external pdfs/ppt/doc files.

when dealing with so much copy, what is the best way to manage/display it? in the first round of this project, i was simply putting it in flash type, with thumbnail images scattered throughout.

it worked, but seemed a little bit archaic. often, with such heavy copy (3 full page scrolls), the thumbnails wouldn’t align where i wanted them, and would end up overlapping with text.

what would y’all recommend?