Never really went that far, so I have no idea... but some guesses
- Number of pages: should be possible to have fairly high numbers there, as the basic page description has a very low memory footprint.
- Might be a better idea to do this inside a loaded swf. To not block the engine while loading there's a short forced delay between initialized elements, so after a certain number of elements it just takes a lot of time to initialize all links (in the case they're realized using <area>s e.g.)... I've two pages each with roughly 100 areas in my test book, and it takes about 3 seconds (looks funny seeing them load sequentially, though [they have an overlay]).
- Flash itself has a limit regarding image sizes, which is 2880x2880 if I'm not mistaken. If it's bigger than that buffering won't work anymore, and who knows what else.
- Maxzoom: no idea, feel free to try

- You'd probably run into memory limits before running into indexing ones. Can't estimate any numbers, though.
- See links.
- Transparency: no actual limit, it's just a matter of how fast the machine you're using is. Transparency is one of the best way's to kill performance in Flash, though, so not many layers, I'd say.
- Loaded pages: indeed, this is a memory / ram thingy, thus depends on the client machine.