Trying this out right now. It didn't go exactly as you said, a few steps were in reverse order for me, but hopefully it works!
EDIT: I watched a movie on my iPad last night that I converted with Format Factory with your method, and it was perfect!
I have not used Format Factory ever. If you are talking about converting video files for iPad, I always using Appgeeker, a nice tool has both windows and mac version.
It also comes with some nice features like settings for various devices.
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