Do you have an Accounts button at the top left of the notes app when in landscape view? If so, tap it and see if all your notes are in iCloud (or other synced account), or local. If the notes that did not sync are in a different area/account, that's probably the reason. I'd need to know more to make a more accurate guess, or suggest an optimum solution.
I don't know about the apps, but if they are compatible with iOS6 (and still available on the App Store) you should be able to go to the Purchased tab in the App Store and download them again.