Hey,
Unfortunately, I don't know flash. I'm familiar enough with graphics editing through Final Cut and Photoshop.
Some of the archival items (such as 300-year old books) may not be easily moveable or matte-box-able. I was thinking that maybe a good still picture scanned well might serve better for such items, and perhaps for collections of more easily manipulated items use the camera.
In general, I agree with the comment that it is often better to leave most effects until post, in case one needs to change one's mind, though with a documentary I think I would tend to shoot archives twice, once still and once with a pan, etc just to give myself more options.
In this case, I want to make the post as easy as possible, since much time will be requirted on the audio, and on a few choice graphics. But maybe I'll invest in both a scanner and a matte-box...
Peace
Jason