I know this is a somewhat old thread, but I'm interested to see if anyone else is having an issue like this.
I work on the program Decipher Backup Repair, that fixes the errors in an iTunes backup so that you can restore your device in iTunes. I'd be very interested to know if anyone thinks they're having a restore issue because of notes, calendar, or contacts and iCloud. Those settings shouldn't affect how the restore works with iTunes as suggested above, but obviously if they are interfering, I would love to integrate a fix into our software. If your backup isn't restoring, and you think it might be related to an issue like this, I hope you'll try Decipher Backup Repair:
http://deciphertools.com/download-decipher-backup-repair.html
And if it doesn't work, contact us at http://deciphertools.com/support.html so we can figure out what is going wrong with your restore! Please mention my name directly, Kelly, so that your note gets directed to me for sure! 🙂
(Note: As I mentioned, I work for the company I've discussed above, so I stand to benefit, either financially or otherwise, from the links I'm recommending.