Alright so I ran through most of your tests from your list.
- booted recovery from fastboot (did not flash)
- performed system backup
- mounted USB storage from within recovery and pushed test zip from OP
- installed updated zip confirming files flashed to system and data (did not confirm cache but one can assume)
- performed system restore to prior state
- reboot to recovery (note being that I did not flash CWM at this point it booted into TWRP)
- reboot device; at this point the device looped back into recovery
- set bootmode from adb back to 4000 and reboot device
- booted recovery from fastboot again
- reboot to fastboot mode
- reboot device
- flashed and booted back into recovery
- reboot into recovery mode (curious if there would be a difference between having TWRP flashed on the device)
- reboot device again, device did reboot properly this time.
In short: AWESOME!!!
Edit:
So I've been playing around a bit with a few other things tonight, went to make another backup from within CWM and I only had 150megs of space free (oops), no big deal right?
Went into mounts and storage and mounted the usb from my PC and deleted some older backups from twrp.
Unmounted the device and went to make another backup... 0megs of space free. (I went ahead and remounted the usb and deleted the partial backup that had been made) and checked again, still 0 (the PC of course shows over a gig free at this point)
Reboot > reboot recovery. USB is remounted properly and the correct amount of space is displayed.
Appears to be a small issue with the device remounting the sdcard after externally modifying the contents.
Unfortunately I've already rebooted so I don't think the recovery logs will be much use but for the sake of testing I would be more than willing to fill my sdcard backup with random junk and reproduce the error again? lol