Reinstall default apps on Galaxy S3 before updating to Jelly Bean
Depending on what network you are on the official OTA update may be your easiest answer. When I updated my razr m  from ICS to JB 4.1 on verizon with the offical JB OTA update, none of my data was lost, didn't have to reload any apps, or reset options. 

Also when you clear your user data your phone may automatically re-download apps that you previously had. In my case when I cleared my user data to root my phone, it re-downloaded all the apps I had before the clear but unfortunately the options for the apps were reset. 

You may want to try clearing only your cache first (that will not erase any contacts or apps) and try reinstall again.