gdgt

I have not found anything that will do it automatically. Going under the assumption that you used calibre to convert the files at mobi file then in itunes, with your ipad connected, select your iPad and go to the Apps tab. Then at the bottom in the File sharing area select the Kindle item on the left and you can drag items into the list on the right. Or you can use the add button to put additional files in. This is in no way automated but it will get the files onto your ipad in the kindle app. Now on the other hand if you want automatic then you could use something like goodreader with your dropbox account and save all your ebooks you create as .pdfs in a dropbox folder that you set to sync. not the same reader experience with dynamic scaling but it kinda makes it up to you if you want automatic sync or a clean reader experience more.

even with this solution you still don't get the whispersync function between your devices for items that you created yourself.