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The best solution I have found is this. It's not Calibre Companion, but it will get your eBooks onto your iPad. You'll need Dropbox on your iPad and the computer that has Calibre. You'll also need the Marvin reader app on your iPad.
In Calibre, click Connect/Share and then Connect to Folder. Choose your Dropbox folder, or create a folder in Dropbox for your books and choose that. Send any or all your Calibre books to the Dropbox folder. Give them a chance to upload to the Dropbox server.
Then, in Marvin, choose Get Books and then Dropbox. All books in your Dropbox can now be imported into Marvin. Marvin is a very good iOS reader app. You can use Calibre to convert your books to ePub or other formats Marvin supports before sending them to Dropbox.
You can't organize your books in Marvin in the same ways you can in Calibre Companion, but you'll find that Marvin is very customizable. It's easy to find settings that are best for your eyes.
You may be able to use iTunes to get books onto your iPad, but I haven't used that method.
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