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The first thing I'd test is if Adobe Acrobat Reader can open your AI files. If not, game over.
Personally, I'd render these things down to high-res transparent PNGs and do the layering in ActionScript, drawing them on a canvas with the proper stack-up. The Flash platform's drawing mechanisms do scaling, transparency and antialiasing very well,
Well, I know that Reader can open PDF files with layers set up in Illustrator. So that means "game on".
As for your idea of transparent PNGs, that might work fine if we weren't looking to a huge quantity of drawings. We'd like to be able to bring in PDFs because there are going to be so many files! We'd like to have an interface which allows a user to open a file from a menu/interface and then see the PDF right there, access the layers and turn them on/off as they need for printing without being able to take the data and use it for themselves in Illustrator (basically ripping our data off).