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As a Graphic and Web Designer by trade I have to say this.
For the love of god do not set your PDF file to print graphics at 1200dpi, you will end up with a huge file that will take an age to download and render on most screens. Plus would take the average office printer a very long time to print. There is a direct colleration between size of graphics and the size of the PDF file, optimal use for PDF is to try to keep it under 1MB for web downloads. Unless of course you have a very understand webhost over bandwidth usage (and even unlimited does have a cap).
Couple of rules of thumb about web graphics.
Graphics displayed on a computer screen do not need to be any more 72dpi, and very rarely need to be wider than 640px unless your running a full screen banner image then up 1000px will fill out most screens. Why 72dpi? Screen resolutions work at that and it gives you the optimal size and graphic quality for most web applications.
When you do traditional printing you can actually get away with 72dpi with BW printing, but the recommended dpi is a minimal 150, at best you should aim for 300dpi. Keep in mind the medium your printing on, 1200dpi? Your not doing a billboard!
Although I did skim through most of this thread, I don't really understand exactly what you are doing. An interactive eBook is what I got out of this. Not sure if a lot of the current tech in eReaders are up to this as this all reads as a huge web application, but multiple formats is a good place to start.
For that if someone else can do the heavy lifting for you for a backend fee, then let them.
Beyond that good luck, and I hope you discover what you really want to do.
Arigato,
Nick Davis
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