I originally updated to 3.1.3 and then ran Spirit, it was fine and dandy, but reboots would take forever (15-20 minutes). I decided to try to a restore to defaults and reran spirit and it is fine now. IMO, it is better to RESTORE rather than UPDATE. Also, if you are worried about your JB apps, install Rock and allow it to back up your apps. Just be sure to add any repo's if you've added them manually so it can grab them for you.