This is a great thread, I think I may have found most of my solution reading through it. Let me start from the beginning:
I was running ICS 4.0.4, stock rom, and rooted. I wanted to upgrade to JB, so I flashed the JB leak. From TWRP I: factory reset, wipe cache, wipe dalvic, flashed rom, flashed modem, flashed root recovery.
Upon restarting I reinstalled Titanium Backup and restored system data, apps and app data. Ever since I've had a problem crop up: at random times (once or twice a day) it will completely freeze up. I notice it when I go to wake it up and it's completely unresponsive. I have to hold the power button down for a few seconds a few times before it finally starts booting up again. (It also somehow killed my 32gb sd card).
Reading through this thread, it sounds like my problem was restoring the system data and app data. My girlfriend has the same phone, and I went through the same process that I did on mine, and she is having the same problem (except for the sd card).
Do you think if I flash the official jb update and don't restore the system data & app data that we'll be free of this problem? Would I have to go through the whole process of factory reset and cache wiping?