I am using 3D graphics for my book too. I am almost finished and I might as well share some of my discoveries using iBooks Author.
1. So far I have read that you should make your images larger than the ratio of the ipad. Since the iPad 3 has a retina display (2048x1536) render images at this resolution, since iPad 2 will downsize it anyway. The cover image is 600x800. Since no one can actually zoom in on this image, it doesn't have to be HD like the other pages. (If you see a real ibook, it shows the cover for about 2 seconds and then opens the book).
2. I have read that JPG is the best image file to use since you can reduce the file size and keep the resolution while PNG you can't.
3. WIth the 3D widget, I think .OBJ is the file you can use.
4. All you need is iBooks author, assuming you have updated your mac to 10.7.2. You must have MAC OSX lion, ibooks author and download iTunes Producer (an app to send your book to itunes) iBooks 2 reader app and an ipad with iOS 5.1. Assuming you are going to make an interactibe book, you may need iWorks 09 to make Keynote stuff to add it. You will need an audio editor and a ePub compatible text editor to edit the code (XML) to add read aloud features. (Assuming you don't know what the next steps are, you will need an ISBN number first soon after you finished the book, second you need your tax id to enter into itunes account, bank account, and then you can submit book. I heard it takes from 2 weeks to 2 months to find out if it has been accepted or rejected. It can be rejected by simply having the word "iBooks" in your text, as an example).
Hope this helps, this is an overview of everything you will need to go from ibook author to published ibook. Here is another tip, you won't get much info on the deeper parts of ibooks author. You will have to learn them yourself or talk to someone who has already finished an ibook and get tips from many sources. No one source will have all the info you need, yet. Here are some more resources:
iBooks Author: Publish your book to the iBookstore
How to Sell iBooks in iTunes Producer - YouTube
How To Write Your First Book In iBooks Author
Apple Will Own Your Work With iBooks Author
How to Create Fixed-Layout iBooks, Part 1 - The Adventures of an ...