I'm certainly no expert but came across this http://blogs.creative-jar.com/post/My-ordeal-with-the-iPad2c-iBooks-and-video-embedding.aspx
You may find it useful.
get iBooks Author free from the mac app store, it allows you to make iBooks and embed video and other media
i did do some testing today in an app by Readdle called PDF expert. It was able to run mp4 embedded in a pdf page. Trouble is, it's $9.99