3GS updated to 5.1 and now no contacts most all apps close as they attempt to open

Thought it all went well until this morning, I can text. Its hooked up to the USB to PC and Itunes sees it fine but the phone sez charging not supported with this accessory.
Doesn't it do a backup of my phone before it upgrades? How do I restore it to that backup?

Yeah this was my first time connecting my phone to the computer since I went to iOS 5.0 and iCloud, so I wasn't familiar with the fact that it did not automatically create a backup on iTunes during the Sync process.  Should have right-clicked on the phone device and did a manual backup.
But still, after restoring the backup from iCloud, I don't understand why data from certain apps got hosed (anything before October 2011, which was my last iTunes backup), while other apps' data appears to be fully intact.

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