As for the notes:
In the Mac OS Mail app. You might need to click the expansion triangle next to Reminders in the sidebar on the left. You can also have them show up in the Inbox if you check the box in Preferences > Accounts tab > Mailbox behaviors.
As for the home page bookmarks, I'm not sure. These should have been moved back over when you restored your info. Or did you set it up as s new device?
If so, you may need to recreate them. The best way to keep those would be to add them to the regular Bookmarks (and "sync bookmarks" in iTunes is turned on -> device name ->Info -> Sync Bookmarks).
Then after the regular bookmark is saved, add it to the home screen. That way you'll always have the bookmarks stored, even if you restore to factory settings...they'll still be on the Mac.