Okay I left it on the charger for an hour, booted into recovery, wiped cache/dalvik cache and fixed permissions, rebooted, and once again after 5 minutes of "starting apps" nothing has happened (although it upgraded 121 apps this time instead of 12).
Round 2. Booted into recovery, wiped cache/dalvik cache, flashed the PA ROM zip and the PA gapps, and rebooted (I didn't even flash Franco's kernel this time). I got past the PA loading screen and my phone has been "starting apps" for the last 10 minutes. Still going as I write this.
Any more ideas?
Well, if you have a nandroid that is recent enough that you wouldn't lose much data going back to it, I would do a full wipe: system, factory reset, cache and dalvik cache in recovery. Then fresh flash ROM and GApps. See what happens.
Now this is just speculation but you may have some data corruption going on. Before you fresh flash, you may want to boot into recovery and do an adb pull command to get all data copied yo your computer.
In terminal, CD to your platform-tools folder. This is where your adb and fastboot utilities live. Then, while the phone is connected and in recovery, type sudo adb pull /sdcard/0/ /your directory of choice to copy these files/
Now if you want to ensure that you have no data corruption, type sudo adb reboot bootloader
Now you should be in the bootloader with a Big Android laying on his back and your device info in the bottom left corner. Now lock and unlock the bootloader to wipe the sdcard. Type sudo fastboot oem lock
Now type sudo fastboot oem unlock
Volume up once and power button to unlock the bootloader. Now we need to reflash your recovery. Make sure you have a recovery image downloaded (I really recommend using TWRP; find it on goo.im) and in your platform-tools folder. For ease, name it recovery.img Use this command: sudo fastboot flash recovery /recovery.img
Now you can volume up a couple times and you should see recovery in red at the top right. Hit the power button to boot into recovery. Now in recovery, copy back ROM, GApps and a su.zip file. Make sure you have each file in your platform-tools folder, so you may need to copy those over from where you saved the contents of your sdcard earlier.
Use these commands:
sudo adb push /su.zip /sdcard/0/Download
sudo adb push /name of ROM file.zip /sdcard/0/Download
sudo adb push /name of GApps file.zip /sdcard/0/Download
Now flash the su file first. Now do a full wipe. Now flash ROM, then GApps.
If this doesn't work, I'd be amazed. I've had to do this before so I know it will work. Let me know if you run into any problems or have questions.
jmar